Protein Structure Modeling * Protein structure prediction and why is it useful?
* An overview of protein structure prediction
* Application: Structure-based drug design
An overview of protein structure prediction:
Protein structure determination methods:
X-ray crystallography
Accuate
Must have 20 mg material
Must be able to crystallize protein
NMR Limited to about 120 residues
Protein must be soluble, about 30mg/ml
Protein structure prediction
Does not need material
Complementary to Crystallography/NMR
More information=higher reliablity
Prediction categories: * Second structure prediction-1D only
* Protein threading or fold family recognition-3D fold information
* Homology modeling-up to X-ray accuracy
* Ab-initio structure prediction-3-6 A
Secondary Structure Prediction:
* Given an amino acid sequence
Predict a secondary structure state (alpha helix, beta strand, coil) for each residue in the sequence
* Best prediction method: PSIPRED (Jones)
* Provides more information for threading and other 3D prediction approaches
* Assists in structure determination
Threading:
* Given:
sequence of protein P with unknown structure
Database of known folds
* Find:
Most plausible fold for P
Good alignment gives approximate backbone structure
* Places the residues of unknown P along the backbone of a known structure and determines stability of side chains in that arrangement
Homology Modeling:n
* Simplest, reliable approach
* Basis: proteins with similar sequences tend to fold into similar structures
* Has been observed that even proteins with 25% sequence identity fold into similar structures
* Does not work for remote homologs (< 25% pairwise identity)
* Given:
A query sequence Q
A database of known protein structures
Find protein P such that P has high sequence similarity to Q
Return P’s structure as an approximation to Q’s structure
How good can homology modeling be?
Sequence Identity Accuracy
60-100% Molecular replacement in crystallography
Support site-directed mutagenesis
through visualization
30-60% Comparable to medium resolution NMR
Substrate Specificity
<30% Serious errors
Successful homology modeling program:
COMPOSER – felix.bioccam.ac.uksoft-base.html
MODELLER – guitar.rockefeller.edu/modeller/modeller.html
WHAT IF – www.sander.embl-heidelberg.de/whatif/
SWISS-MODEL – www.expasy.ch/SWISS-MODEL.html
For more information:
Comparative protein structure modeling with Modeller: A practical approach by Andras Fiser and Andrej Sali
Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3D model for a protein (target) that is related to at least one known protein structure (template) [1,2,3,4,5,6,7].
Despite progress in ab initio protein structure prediction [8], comparative modeling remains the only method that can reliably predict the 3D structure of a protein with an accuracy comparable to a low-resolution experimentally determined structure [6]. Even models with errors may be useful, because some aspects of function can be predicted from only coarse structural features of a model. Typical uses of comparative models are listed in Table 1 [4,6].
3D structure of proteins from the same family is more conserved than their primary sequences [9]. Therefore, if similarity between two proteins is detectable at the sequence level, structural similarity can usually be assumed. Moreover, proteins that share low or even non-detectable sequence similarity many times also have similar structures. Currently, the probability to find related proteins of known structure for a sequence picked randomly from a genome ranges approximately from 20% to 65%, depending on the genome [10,11]. Approximately one half of all known sequences have at least one domain that is detectably related to at least one protein of known structure [10]. Since the number of known protein sequences is approximately 600,000 [12,13], comparative modeling can be applied to domains in approximately 300,000 proteins. This number is an order of magnitude larger than the number of experimentally determined protein structures deposited in the Protein Data Bank (PDB) (15,000 ) [14]. Furthermore, the usefulness of comparative modeling is steadily increasing because the number of different structural folds that proteins adopt is limited [15,16,17,18] and because the number of experimentally determined new structures is increasing exponentially [19]. This trend is accentuated by the recently initiated structural genomics project that aims to determine at least one structure for most protein families [20,21]. It is conceivable that this aim will be substantially achieved in less than 10 years, making comparative modeling applicable to most protein sequences.
Structure modeling flowchart:Ab-initio structure prediction:
* Can be done with any protein…no other members of the family need be known
* Based on assumption – Native State is at the global free energy minimum
* Provides a way to observe the motion of large molecules such as proteins at the atomic level – dynamic simulation
* Newton’s second law applied to molecules
* Force on all atoms can be calculated, given this function
Trajectory of motion of molecule can be determined
Monday, February 15, 2010
Saturday, December 19, 2009
BIOINFORMATICS DATABASES AND TOOLS
DATABASES
DatabasesGeneralized (DNA, proteins and carbohydrates, 3D-structures)
Specialized (EST, STS, SNP, RNA, genomes, protein families, pathways, microarray data ...)
Database search
Text-based (SRS, Entrez ...)
Sequence-based (sequence similarity search) (BLAST, FASTA...)
Motif-based (ScanProsite, eMOTIF)
Structure-based (structure similarity search) (VAST, DALI...)
Mass-based protein search (ProteinProspector, PeptIdent, Prowl …)
Analysis toolsDNA sequence analysis tools
RNA analysis tools
Protein sequence and structure analysis tools (primary, secondary, tertiary structure)
Tools for protein Function assignment
Phylogeny
Microarray analysis tools
Miscellaneous
Literature search
Patent search
Bioinformatics centers and servers
Links to other collections of bioinformatics resources
Medical resources
Bioethics
Protocols
Software
(Bio)chemie
Educational resources
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Generalized DNA, protein and carbohydrate databases
Primary sequence databases
EMBL (European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK)
GenBank (at National Center for Biotechnology information, NCBI, Bethesda, MD, USA)
DDBJ (DNA Data Bank Japan at CIB , Mishima, Japan)
Protein sequence databases
SWISS-PROT (Swiss Institute of Bioinformatics, SIB, Geneva, CH)
TrEMBL (=Translated EMBL: computer annotated protein sequence database at EBI, UK)
PIR-PSD (PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA)
UniProt (Joined data from Swiss-Prot, TrEMBL and PIR)
UniRef (UniProt NREF (Non-redundant REFerence) database at EBI, UK)
IPI (International Protein Index; human, rat and mouse proteome database at EBI, UK)
Carbohydrate databases
CarbBank (Former complex carbohydrate structure database, CCSD, discontinued!)
3D structure databases
PDB (Protein Data Bank cured by RCSB, USA)
EBI-MSD (Macromolecular Structure Database at EBI, UK )
NDB (Nucleic Acid structure Datatabase at Rutgers State University of New Jersey , USA)
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Specialized databases
Specialized sequence databases
dbEST (Database of Expressed Sequence Tags at NCBI, USA)
TGI (TIGR Genome Indices, integrated analysis of public EST data, TIGR, USA)
Mendel ESTs (Database of annotated plant ESTs in dbEST at JIC, Norwich, UK)
Bodymap (Human and mouse genome expression database (ESTs) at University of Tokyo, JP)
dbGSS (Database of Genome Survey Sequences at NCBI, USA)
dbSNP (Database of Single Nucleotide Polymorphisms at NCBI, USA)
SNPper (SNP explorer by Children's Hospital Informatics Program, Boston, USA)
dbSTS (Database of Sequence Tagged Sites at NCBI, USA)
HGVBASE (Human Genome Variation database, European consortium involving the Karolinska Institute (Sweden), EBI (UK) and EMBL (Germany)
RNA databases
ssu and lsu rRNA database (European ribosomal database at University of Ghent, Belgium)
RDP (Ribosomal database Project, Michigan State University, USA)
miRNA Registry (microRNA registry at the Sanger Insitute, UK)
Genome databases
GOLD (Genomes On Line Database: list of all complete and ongoing genome projects worldwide at University of Illinois, USA)
Genomes at NCBI (NCBI, USA)
Organism Specific Databases (at CMS Molecular Biology Resource, SDSC, USA)
TIGR Database (TDB) (The Institute for Genomic Research, Rockeville MD, USA)
Microbial Genomes (Completed microbial genomes in GenBank and links to genomes in progress)
PEDANT (Browse computationally analyzed completed and unfinished genomes at MIPS, Munich, Germany)
Ensembl (Automatically annotated genomes at EBI, UK)
GeneQuiz (Highly automated analysis of completed genomes at EBI, UK)
HAMAP (Highly automated microbial annotation of proteins at ExPaSy, CH)
UK CropNet (UK Crop Plant Bioinformatics Network, at JIC, IGER, NASC and SCRI, UK)
ArkDb (Livestock animal genome and mapping database at Roslin Institute, Edinburg, UK)
MITOP (MITOchondria Project, database mitochondria-related genes, proteins and diseases at MIPS, Munich, Germany)
Codon Usage Database (Organism specific codon usage database at Kazuasa DNA Research Institute, Jp)
GeneCensus (Comparative genomics database at Yale University, USA)
• Model organism databases
Escherichia coli
E. coli Genome Center (Wisconsin University, USA)
The E. coli index (University of Birmingham, UK)
S. cerevisiae (Baker's yeast)
SGD (Yeast genome database at Stanford, USA)
CYGD (MIPS Comprehensive Yeast Genome Database, Neuherberg, Germany)
Arabidopsis thaliana
MATDB (MIPS A. thaliana database, Munich, Germ.)
TAIR (The Arabidopsis Information Resource, previously AtDB, at Stanford, USA)
KAOS (Kazusa Arabidopsis data Opening Site at Kazusa DNA Research Institute, Jp)
Arabidopsis Genome Analysis (at Cold Spring Harbor laboratories, USA)
TIGR Arabidopsis thaliana Database (TIGR, Rockeville MD, USA)
Oryza sativa (Rice)
RGP (Rice Genome Research Programme, Jp)
Gramene (Comparative mapping resource for graines)
INE (Integrated rice genome explorer: common database of the International Rice Genome Sequencing Project, IRGSP, Jp)
Caenorhabditis elegans
WormBase (C. elegans database at Cold Spring Harbor Laboratories, USA)
Drosophila melanogaster (Fruit fly)
FlyBase (Drosophila genome database)
BDGP (Berkeley Drosphila genome project)
Danio rerio (Zebrafish)
ZFIN (Zebrafish Information Network at University of Oregon, USA)
WashU-Zebrafish Genome Resources (Zebrafish EST database at Washington University, USA)
Mus musculus (Mouse) MGI (Mouse genome informatics)
Homo sapiens
GDB (The human Genome Database, Toronto, Canada)
HIB (HumanInfoBase of annotated UniGene clusters - putative human gene transcripts - at MIPS, Germany)
Human genome resources (at NCBI, USA)
Human genome browser (at the University of California Santa Cruz, USA)
HGP (Human Genome Project at the Sanger Institute, Cambridge, UK)
GeneLinks (Portal to hyperlinks for each human gene at the Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden)
Specialized protein databases
• Proteome databases Proteome analysis (comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms at EBI, UK)
<strong>• Specific protein family databasesProweb (Guide to specific protein families)
TRANSFAC (Transcription Factor Database, housed at Biobase)
GPCRDB (G-Protein Coupled Receptor Database)
PKR (Protein Kinase Resource)
ENZYME (Enzyme database at ExPASy, CH) MEROPS (Peptidase database at Sanger Institute, UK)
Prolysis (Protease and inhibitors database, Univ of Tours, Fr)
CAZy (Carbohydrate-active enZymes at CNRS, Fr)
PROMISE (Prostetic groups and Metal Ions in protein active sites database at Scripps Researche Institute, USA)
ReLiBase (database system for analysing receptor/ligand complexes deposited in the Protein Data Bank at EBI, UK)
IMGT (ImMunoGeneTics database of Igs, TcRs, and MHC molecules at Montpellier, France)
REBASE (Restriction enzyme database at New England Biolabs, USA)
• Protein classification databases CluSTr (Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK)
Pfam (Protein families database of alignments and HMMs at the Sanger Centre, UK)
TIGRFAMs (Protein families based on HMMs at TIGR, USA)
Hits (Protein domain database at ISREC, Switzerland)
SCOP (Structural Classification of Proteins according to familiy, superfamily, common fold, and class)
CATH (Protein structure classification based on Class, Architecture, Topology, and Homologous superfamilies)
BioSpace (Unified sequence-structure classification of proteins, Stanford, USA)
LPFC (Library of Protein Family Cores)
Dali (Dali Fold classification based on structure-structure alignment of proteins, at Helsinki University, Finland)
ENZYME (Enzyme nomenclature database at ExPASy, CH)
strong>PRESAGE<Enzyme Structures Database /strong> (Annotated protein structure database at the University of California, Berkeley, USA)
CDD (Conserved Domain Database at NCBI, USA)
Specialized structure databases
Protein-Nucleic Acid Recognition Database (at BioInfo Bank, Jp) 3DInSight (Integrated database for structure, property and function of biomolecules at BioInfo Bank, Jp)
MolMovDB (Database of macromolecular movements at Yale University, USA)
Pathway databasesKEGG (Kyoto Encyclopedia of Genes and Genomes at Kyoto Univ. Jp. or at mirror servers)
LIGAND (Chemical database for emzyme reactions at Institute for Chemical Research, Kyoto Univ. Jp)
BRITE (Biomolecular Relations in Information, Transmission and Expression, Kyoto Univ., Jp)
Boehringer Mannheim - Biochemical pathways (Maintained at ExPASy, Ch)
BioCyc (Microbial species-specific integrated pathway/genome database)
WIT (What is There? Integrated pathway/genome database. Registration required)
EMP (Database of Enzymes and Metabolic pathways public server
UM-BBD (Microbial biocatalysis/biodegradation pathways, University of Minnesota, USA)
BRENDA (Enzyme and metabolic database at Univ Cologne, Germany)
SRS (Metabolic pathway database search at EBI, UK)
Microarray databasesArrayExpress (Public repository for microarray based gene expression data at EBI, UK)
GEO (Genome Expression Omnibus: Public repository for microarray based gene expression data at NCBI, USA)
2D-page databases
Gelbank (US department of Energy)
Swiss-2DPAGE (Swiss Institute of Bioinformatics, SIB, Geneva, CH)
Lists of databasesDBCAT (Catalog of more than 500 molecular biology databases at INFOBIOGEN, France )
NAR 31 (1) 2003 (Nucl. Acids Res. biological database issue, papers available through NAR online)
NAR 32 (1) 2004 (Nucl. Acids Res. biological database issue, papers available through NAR online)
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Text-based database search
ENTREZ (Integrated database search for nucleotides, proteins, genomes, structures, populations sets and literature at NCBI, USA)
SRS (Search EMBL, SWISS-PROT, TrEMBL, PIR, PDB, etc. at EBI, UK)
DBGET/LinkDB (Integrated database search of LinkDB at GenomeNet, Kyoto University and University of Tokyo)
SSS (Sequence and structure searching site at Berkeley, US)
Molecules R US (Full text search of the PDB database at NIH)
MIA (Molecular Information Agent searching biological databases to find the existing information about a macromolecule at SDSC, USA)
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Sequence-based database search (sequence similarity search)
BLAST (Basic local alignment search tool at NCBI, USA)
FASTA (Fasta or fastx search at EBI, UK)
MPsrch (Smith-Waterman algorithm-based search at EBI, UK)
BLAST Microbial Genomes (Search finished and unfinished genomic sequences at NCBI)
Genome and proteome FASTA (at EBI, UK)
PIR-NRL3D (Sequence-structure data base search at John Hopkins University, USA)
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<strong>Motif-based database search
Kangaroo (Find sequences matching a given DNA or protein pattern at Mount Sinai Hospital, Toronto, Canada)
ScanProsite (Find protein sequences matching PROSITE or other patterns at ExPASy, CH)
ShapeSifter (Find protein sequences matching EMOTIF patterns at Stanford University, USA)
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Structure-based database search (structure similarity search)
Search_SCOP (Protein structure similarity search in SCOP database)
VAST (Structure-structure similarity search at NCBI, US)
DALI (Protein structure comparison with PDB at EBI,UK)
Finding 3D Similarity by CE (Combinatorial Extension) or CT (Compound Likeness) method at SDSC, USA)
LIBRA (Search sequences homologous to a given structure by Inverse Folding Protocol at NIG, Jp)
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Mass-based protein search
ProteinProspector (Proteomics tools for mining sequence databases in conjunction with mass spectrometry at UCSF, USA)
PeptIdent (Protein identification using pI, Mw and peptide mass fingerprinting data at ExPaSy, CH)
Prowl (Resource for protein chemistry and mass spectrometry at the Rockefeller University NY, USA)
Mascot (Protein identification using mass spectrometry data by Matrix Science, London, UK)
MassSearch (Search SwissProt or EMBL by protein mass after digestion at ETH Zurich, CH)
Mowse (Search the owl protein sequence database with protein fragment information at the HGMP-RC, UK)
PeptideSearch (Protein identification by peptide mapping or peptide sequencing at the EMBL, Heidelberg, Germany)
Lutefisk (Software for the de novo interpretation of peptide CID spectra from Immunex, Seattle, USA)
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DNA sequence analysis tools
Restriction; Detect repeats and unusual patterns
Restrictionmapper
Webcutter (Restriction analysis)
RepeatMasker (Search interspersed repeats and low complexity sequences)
REPuter (Fast computation of maximal repeats in complete genomes at Bielefeld University, Germany)
dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
Align (Pairwise sequence alignment with GAP, SIM Align sequences(DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
MAP (Multiple alignment of (long) sequences without penalizing large gaps)
ClustalW (at EBI, UK)
Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
Find genes
Sixframe (Translate DNA sequence in all 6 possible frames at Baylor College of Medecine, USA)
ORF Finder (at NCBI)
GeneMark (Species-specific search for genes at Georgia Institute of Technology , USA)
GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
GenLang (Exon recognition at University of Pennsylvania, USA).
GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
Find transcriptional elements
Identification of Prokaryotic/Eukaryotic Promoters (Promotor prediction in <100 kb DNA at Lawrence Berkeley National Laboratory, USA)
SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA)
FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA))
Find tRNA
tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, Fr)
Other tools
CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
MAR-Wiz (Search for matrix association regions at NCGR, Santa Fe, USA)
Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)
DNA folding server (Fold secondary structures)
PRIDE (Primer design at DFKZ, Heidelberg, Germany)
Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
PCR primer selection
Primer3 (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)
GeneFisher (Interactive PCR primer design tool at the University of Bielefeld, Germany)
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer design at the Weizmann Institute, Israel)
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RNA analysis tools
RNA Fold (Fold your own RNA sequences)
RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)
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Protein sequence and structure analysis tools
Physicochemical properties
ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
Analyse primary sequence
ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
SignalP (Prediction of peptide signal sequence at CBS, Denmark)
TargetP (Prediction of subcellular localization at CBS, Denmark)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
NetPhos (Prediction of phosphorylation sites in eukaryotic proteins at CBS, Denmark )
Scansite (Prediction of phosphorylation sites and protein binding sites at MIT, Cambridge, USA)
Helical Wheel (Representation of alpha-helical peptides)
Other primary sequence analysis tools at ExPaSy
Alignment
• Pairwise
Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
Pairwise sequence alignment (at Baylor College of Medecine, USA)
Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
• Multiple
ClustalW (at EBI, UK)
ClustalW (at the Baylor College of Medicine, USA)
MAP (Multiple alignment of (long) sequences without penalizing large gaps)
Multiple sequence alignment (at Baylor College of Medecine, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
Predict secondary structure
TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
SOSUI (Prediction of Transmembrane Regions, JP)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
PredictProtein (Protein secondary structure prediction at EMBL)
JPred (Protein secondary structure prediction at Dundee University, UK)
HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
PSIpred (Protein secondary structure prediction at Brunel University, UK)
nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
Other secondary structure prediction tools at ExPASy
BTPRED (Prediction of beta-turns at UCL, UK)
Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
PairCoil (Prediction of coiled Coil regions by Berger's method)
MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)
TOPS (Protein topology cartoon generation at University of Leeds, UK)
Analyse and model 3D structure
• 3D viewers
RasMol (Free offline 3D viewer. Download)
Swiss-Pdb Viewer (Deep View) (Free offline 3D viewing and analysis application, tightly linked to Swiss-Model. Tutorial)
Chime (Browser plugin for structure view from MDL Chemscape)
Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)
WebMol (Online 3D viewer at University of California, USA)
3D analysis
TOPS (Protein topology cartoon generation at University of Leeds, UK)
DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
OCA (Structure database browser at EBI, UK)
STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)
PsiPred (Sequence profile based fold recognition at Brunel University, UK)
Predicting Protein 3D structure based on homologous sequence search (EMBL Heidelberg, Germany)
123 (Fold prediction by aligning (threading) to a (set of) structure(s)
LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
CE (3-D protein structure comparison and alignment using the combinatorial extension (CE) method at SDSC, USA)
DALI (Automated Protein Structure Alignment at EBI,UK)
LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
VAST (Structure-structure similarity search at NCBI, US)
ASC (Analytic Surface Calculation of PDB molecules at IMP, Vienna)
MolSurfer (Calculate and navigate protein-protein interfaces at EML, Germany)
Protein-Protein Interaction Server (UCL, UK)
3D homology modeling
CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)
Swiss-Model (Automated protein homology-modeling server at ExPASy, Switzerland)
3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
FAMS (Fully Automated Modeling Service at Kitasato University, JP)
3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
SDSC1 (Protein structure homology modeling server at SDSC, USA)
Meta PP (Collection of structure prediction services at Columbia University, USA)
List of comparative modeling tools (at the Rockefeller University, NY, USA)
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Tools for protein function assignment
Scan or search for patterns, motifs, profiles, domains, families
ScanProsite (Scan a protein sequence against PROSITE pattern database at ExPASy, CH)
PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
PFSCAN (Scan protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)
BLOCKS Search (Scan a protein against BLOCKS database; also searches PRINTS)
eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies at Stanford University, USA)
Scansite (Prediction of protein signaling sequence motifs at MIT, Cambridge, USA)
MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
eMotif-maker (Build motifs that describe protein families or superfamilies at Stanford University, USA)
Meta-MEME (Buid motif at San Diego Supercomputer Centre, SDSC, Ca, USA)
CDART (Conserved Domain Architecture Retrieval Tool at NCBI, USA)
SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST at NCBI, USA)
COGnitor (Search a protein agains the COG database at NCBI)
iProClass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
ConSurf (Identification of functional regions in proteins by surface-mapping of phylogenetic information at Tel Aviv University, Israel)
ProDom (Automatically generated protein domain database at Toulouse, Fr)
Modules (Mobile protein domains database at EMBL)
SBASE (Protein domain library at ICGEB, Trieste, It)
HSSP (Database of homology-derived structures and sequences of proteins at EBI)
3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Chime plugin))
eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
GeneQuiz (Automated analysis of protein sequences at EMBL)
Search, computation and analysis of pathways
KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
aMAZE (Query tools for metabolic and signal transduction pathway analysis at ULB, Belgium)
Protein-protein interactionsDIP (Search Database of Interacting Proteins at UCLA, USA)
PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Canada)
BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Canada )
BINDBLAST (Search BIND database with BLAST)
MINT (Molecular INTeraction database at Rome University, It)
GRID (General Repository of Interaction Datasets at the Samuel Lunenfeld Research Institute, Canada)
PPI viewer (Mammalian protein-protein interaction database and viewer at RIKEN, Japan)
STRING (database of predicted functional associations among genes/proteins at the EMBL)
InterPrets (Interaction prediction through structure at the EMBL)
Protein Annotation
PAA (Protein Annotator's Assistant at EBI, UK)
AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Institute, UK)
Gene Ontology tools (Universal function annotation vocabulary by the Gene Ontology Consortium )
Automatic alert for related new sequence
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
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Phylogenetic Analysis
Multiple sequence alignment
ClustalW (Multiple sequence alignment at EBI, UK)
Multiple sequence alignment (at Baylor College of Medecine, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
Entrez-PopSet (Search set of DNA sequences from populations of related individuals/organisms at NCBI)
ConSurf (Identification of functional regions in proteins by surface-mapping of fhylogenetic information at Tel Aviv University, Israel)
Links to phylogeny software tools and servers (at the University of Washington, USA)
Organism classification
NCBI Taxonomy
The Tree of Life Project
TreeBASE (database of phylogenetic knowledge hosted by the University at Buffalo, USA)
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Microarray Data Browsing and Analysis
ArrayExpress (Repository for microarray data at EBI, UK)
GEO (Gene Exprssion Omnibus at NCBI)
SMD (Stanford microarray database, including microarray tools and tool links)
YMD (Yale microarray database)
Expression Profiler (Web-based microarray data analysis at EBI, UK)
GenMapp (Free computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes )
TBI Expression Analysis (Find differential genes between two filter hybridisation experiments at DFKZ, Heidelberg)
Other links to public microarray and gene expression databases
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Literature search
PubMed (Search public version of full Medline integrated in ENTREZ at NCBI, USA)
PubMed Central (Free online access to full text of life Science rechearch articles at NCBI, USA)
FreeMedicalJournals (Links to free online medical journals)
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
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Patent search
esp@cenet (Search for National and worldwide patents at European Patent Office)
USPTO (Search for US patents at US Patent and Trademark office)
DPD (DNA Patent Database at Georgetown University, US)
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Bioinformatics centers and servers
ANGIS (Australian National Genomic Information Service)
BEN (Belgian EMBNet Node)
Brutlag Bioinformatics Group (at Stanford University, USA)
CBS (Center for Biological Sequence analysis, Denmark)
CIB (Center for Information Biology, Mishima, Jp)
EBI (European Bioinformatics Institute, Hinxton, UK)
EMBnet and related WWW servers
ExPASy (Geneva, CH)
Genestream (at IGH, Montpellier, Fr)
GenomeNet Japan
ISCB (International Society for Computational Biology)
ISREC (Swiss Institute for Experimental Cancer Research)
MBCR (Biomedical Computing Facility)
MIPS (Munich Information Centre for Protein Sequences, Munich, Germ.)
NCBI (National Center for Biotechnology Information, Bethesda MD, USA)
NCGR (National Center for Genome Resources, Santa Fe, New Mexico, USA)
RFCGR (MRC Rosalind Franklin Centre for Genomic Research, Hinxton, UK)
Roslin Institute Bioinformatics (Edinburg, UK)
Sanger Institute (Hinxton, UK)SBG (Structural Bioinformatics Group at the EMBL, Heidelberg, Germany)
SDSC (San Diego Supercomputer Center, USA)
SHGC (Stanford Human Genome Center)
SIB (Swiss Institute for Bioinformatics, Geneva, CH)
Stanford Genome Technology Center
Stanford Genomic Resources
TIGR (The Institute for Genomic Research, USA)
UCL Biochemistry BSM Group (Biomolecular Structure and Modelling Group, UK)
Washington Genome Sequencing Center
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Links to other collections of bioinformatics resources
BioBencHelper
BIW (BioInformatics Web of Suresh Kumar)
BCM Search Launcher (Interface for related WWW tools at Baylor College of Medicine)
GenomeWeb (at the MRC RFCGR, Hinxton, UK)
HNB (Helmholz Network Network for Bioinformatics, Germany)
Luke's EMBOSS GUI (GUIs to EMBOSS, the European Molecular Biology Open Software Suite for sequence analysis)
AMOS' WWW Page Links (more than 1000 links listed by Amos Bairoch)
ExPASy Proteomics Tools (CH)
CMS Molecular Biology Resource (at San Diego Supercomupter Center, US)
Pack of WWW Tools for Molecular Analysis (at Adelaide University, Australia)
ABIM online Analysis Tools (Université Aix-Marseille, Fr)
Bioinformatics resources CCP11 (MRC, UK)
MolBiol.net (Links directory of bioinformatics, genomics, proteomics, biotechnology and molecular biology )
List of other Molecular Biology Resources
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Medical resources
OMIA (Online Mendelian Inheritance in Animals, University of Sydney, Australia)
OMIM (Online Mendelian Inheritance in Man at the NCBI)
The MERCK Manual of Diagnosis and Therapy (Guide to clinical information)
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Protocols
Protocol Online (Find/submit protocols in molecular biology, cell biology, immunology etc.)
Molecular Biology Protocols (collections of protocols)
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Software
BioCatalog (Software directory of general interest in molecular biology and genetics at EBI, UK)
Logiciels (Software directory at Institut Pasteur with links to providers and tutorials)
Molscript
NCBI Toolbox (NCBI software tools for building bioinformatics resources)
Phylogeny Programs (Collection of phylogeny software and servers)
BioPerl (international association of developers of open source Perl tools for bioinformatics, genomics and life science research)
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(Bio)chemistry
NIST Standard Reference Data Products Catalog
ChemFinder
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Educational resources
S-Star.org (Online Bioinformatics education by a collaboration of 7 universities wordwide)
BioComputing Hypertext Coursebook (Bielefeld, Germany)
Guide to Molecular Sequence Analysis (By Andrew Louka, University of Oslo, Norway)
NCBI Education (Bioinformatics definitions and tutorials at the NCBI, USA)
Molecules in the Classroom (UMass Amherst USA)
DNA Structure
NDB Biomolecular Resource (Nucleic Acid education)
NDB Atlas of Nucleic Acid Containing Structures
Teachers' Molecular Visualization Resources
BioMolecular Structure Education Web Sites
Biochemistry in 3d (Accompanies Lehninger Principles of Biochemistry)
IMAGE (Image library of biological macromolecules from IMB Jena Biocomputing Group, Jena, Germ.)
Protein Crystallography on the Web (University of London, UK)
DatabasesGeneralized (DNA, proteins and carbohydrates, 3D-structures)
Specialized (EST, STS, SNP, RNA, genomes, protein families, pathways, microarray data ...)
Database search
Text-based (SRS, Entrez ...)
Sequence-based (sequence similarity search) (BLAST, FASTA...)
Motif-based (ScanProsite, eMOTIF)
Structure-based (structure similarity search) (VAST, DALI...)
Mass-based protein search (ProteinProspector, PeptIdent, Prowl …)
Analysis toolsDNA sequence analysis tools
RNA analysis tools
Protein sequence and structure analysis tools (primary, secondary, tertiary structure)
Tools for protein Function assignment
Phylogeny
Microarray analysis tools
Miscellaneous
Literature search
Patent search
Bioinformatics centers and servers
Links to other collections of bioinformatics resources
Medical resources
Bioethics
Protocols
Software
(Bio)chemie
Educational resources
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Generalized DNA, protein and carbohydrate databases
Primary sequence databases
EMBL (European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK)
GenBank (at National Center for Biotechnology information, NCBI, Bethesda, MD, USA)
DDBJ (DNA Data Bank Japan at CIB , Mishima, Japan)
Protein sequence databases
SWISS-PROT (Swiss Institute of Bioinformatics, SIB, Geneva, CH)
TrEMBL (=Translated EMBL: computer annotated protein sequence database at EBI, UK)
PIR-PSD (PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA)
UniProt (Joined data from Swiss-Prot, TrEMBL and PIR)
UniRef (UniProt NREF (Non-redundant REFerence) database at EBI, UK)
IPI (International Protein Index; human, rat and mouse proteome database at EBI, UK)
Carbohydrate databases
CarbBank (Former complex carbohydrate structure database, CCSD, discontinued!)
3D structure databases
PDB (Protein Data Bank cured by RCSB, USA)
EBI-MSD (Macromolecular Structure Database at EBI, UK )
NDB (Nucleic Acid structure Datatabase at Rutgers State University of New Jersey , USA)
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Specialized databases
Specialized sequence databases
dbEST (Database of Expressed Sequence Tags at NCBI, USA)
TGI (TIGR Genome Indices, integrated analysis of public EST data, TIGR, USA)
Mendel ESTs (Database of annotated plant ESTs in dbEST at JIC, Norwich, UK)
Bodymap (Human and mouse genome expression database (ESTs) at University of Tokyo, JP)
dbGSS (Database of Genome Survey Sequences at NCBI, USA)
dbSNP (Database of Single Nucleotide Polymorphisms at NCBI, USA)
SNPper (SNP explorer by Children's Hospital Informatics Program, Boston, USA)
dbSTS (Database of Sequence Tagged Sites at NCBI, USA)
HGVBASE (Human Genome Variation database, European consortium involving the Karolinska Institute (Sweden), EBI (UK) and EMBL (Germany)
RNA databases
ssu and lsu rRNA database (European ribosomal database at University of Ghent, Belgium)
RDP (Ribosomal database Project, Michigan State University, USA)
miRNA Registry (microRNA registry at the Sanger Insitute, UK)
Genome databases
GOLD (Genomes On Line Database: list of all complete and ongoing genome projects worldwide at University of Illinois, USA)
Genomes at NCBI (NCBI, USA)
Organism Specific Databases (at CMS Molecular Biology Resource, SDSC, USA)
TIGR Database (TDB) (The Institute for Genomic Research, Rockeville MD, USA)
Microbial Genomes (Completed microbial genomes in GenBank and links to genomes in progress)
PEDANT (Browse computationally analyzed completed and unfinished genomes at MIPS, Munich, Germany)
Ensembl (Automatically annotated genomes at EBI, UK)
GeneQuiz (Highly automated analysis of completed genomes at EBI, UK)
HAMAP (Highly automated microbial annotation of proteins at ExPaSy, CH)
UK CropNet (UK Crop Plant Bioinformatics Network, at JIC, IGER, NASC and SCRI, UK)
ArkDb (Livestock animal genome and mapping database at Roslin Institute, Edinburg, UK)
MITOP (MITOchondria Project, database mitochondria-related genes, proteins and diseases at MIPS, Munich, Germany)
Codon Usage Database (Organism specific codon usage database at Kazuasa DNA Research Institute, Jp)
GeneCensus (Comparative genomics database at Yale University, USA)
• Model organism databases
Escherichia coli
E. coli Genome Center (Wisconsin University, USA)
The E. coli index (University of Birmingham, UK)
S. cerevisiae (Baker's yeast)
SGD (Yeast genome database at Stanford, USA)
CYGD (MIPS Comprehensive Yeast Genome Database, Neuherberg, Germany)
Arabidopsis thaliana
MATDB (MIPS A. thaliana database, Munich, Germ.)
TAIR (The Arabidopsis Information Resource, previously AtDB, at Stanford, USA)
KAOS (Kazusa Arabidopsis data Opening Site at Kazusa DNA Research Institute, Jp)
Arabidopsis Genome Analysis (at Cold Spring Harbor laboratories, USA)
TIGR Arabidopsis thaliana Database (TIGR, Rockeville MD, USA)
Oryza sativa (Rice)
RGP (Rice Genome Research Programme, Jp)
Gramene (Comparative mapping resource for graines)
INE (Integrated rice genome explorer: common database of the International Rice Genome Sequencing Project, IRGSP, Jp)
Caenorhabditis elegans
WormBase (C. elegans database at Cold Spring Harbor Laboratories, USA)
Drosophila melanogaster (Fruit fly)
FlyBase (Drosophila genome database)
BDGP (Berkeley Drosphila genome project)
Danio rerio (Zebrafish)
ZFIN (Zebrafish Information Network at University of Oregon, USA)
WashU-Zebrafish Genome Resources (Zebrafish EST database at Washington University, USA)
Mus musculus (Mouse) MGI (Mouse genome informatics)
Homo sapiens
GDB (The human Genome Database, Toronto, Canada)
HIB (HumanInfoBase of annotated UniGene clusters - putative human gene transcripts - at MIPS, Germany)
Human genome resources (at NCBI, USA)
Human genome browser (at the University of California Santa Cruz, USA)
HGP (Human Genome Project at the Sanger Institute, Cambridge, UK)
GeneLinks (Portal to hyperlinks for each human gene at the Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden)
Specialized protein databases
• Proteome databases Proteome analysis (comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms at EBI, UK)
<strong>• Specific protein family databasesProweb (Guide to specific protein families)
TRANSFAC (Transcription Factor Database, housed at Biobase)
GPCRDB (G-Protein Coupled Receptor Database)
PKR (Protein Kinase Resource)
ENZYME (Enzyme database at ExPASy, CH) MEROPS (Peptidase database at Sanger Institute, UK)
Prolysis (Protease and inhibitors database, Univ of Tours, Fr)
CAZy (Carbohydrate-active enZymes at CNRS, Fr)
PROMISE (Prostetic groups and Metal Ions in protein active sites database at Scripps Researche Institute, USA)
ReLiBase (database system for analysing receptor/ligand complexes deposited in the Protein Data Bank at EBI, UK)
IMGT (ImMunoGeneTics database of Igs, TcRs, and MHC molecules at Montpellier, France)
REBASE (Restriction enzyme database at New England Biolabs, USA)
• Protein classification databases CluSTr (Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK)
Pfam (Protein families database of alignments and HMMs at the Sanger Centre, UK)
TIGRFAMs (Protein families based on HMMs at TIGR, USA)
Hits (Protein domain database at ISREC, Switzerland)
SCOP (Structural Classification of Proteins according to familiy, superfamily, common fold, and class)
CATH (Protein structure classification based on Class, Architecture, Topology, and Homologous superfamilies)
BioSpace (Unified sequence-structure classification of proteins, Stanford, USA)
LPFC (Library of Protein Family Cores)
Dali (Dali Fold classification based on structure-structure alignment of proteins, at Helsinki University, Finland)
ENZYME (Enzyme nomenclature database at ExPASy, CH)
strong>PRESAGE<Enzyme Structures Database /strong> (Annotated protein structure database at the University of California, Berkeley, USA)
CDD (Conserved Domain Database at NCBI, USA)
Specialized structure databases
Protein-Nucleic Acid Recognition Database (at BioInfo Bank, Jp) 3DInSight (Integrated database for structure, property and function of biomolecules at BioInfo Bank, Jp)
MolMovDB (Database of macromolecular movements at Yale University, USA)
Pathway databasesKEGG (Kyoto Encyclopedia of Genes and Genomes at Kyoto Univ. Jp. or at mirror servers)
LIGAND (Chemical database for emzyme reactions at Institute for Chemical Research, Kyoto Univ. Jp)
BRITE (Biomolecular Relations in Information, Transmission and Expression, Kyoto Univ., Jp)
Boehringer Mannheim - Biochemical pathways (Maintained at ExPASy, Ch)
BioCyc (Microbial species-specific integrated pathway/genome database)
WIT (What is There? Integrated pathway/genome database. Registration required)
EMP (Database of Enzymes and Metabolic pathways public server
UM-BBD (Microbial biocatalysis/biodegradation pathways, University of Minnesota, USA)
BRENDA (Enzyme and metabolic database at Univ Cologne, Germany)
SRS (Metabolic pathway database search at EBI, UK)
Microarray databasesArrayExpress (Public repository for microarray based gene expression data at EBI, UK)
GEO (Genome Expression Omnibus: Public repository for microarray based gene expression data at NCBI, USA)
2D-page databases
Gelbank (US department of Energy)
Swiss-2DPAGE (Swiss Institute of Bioinformatics, SIB, Geneva, CH)
Lists of databasesDBCAT (Catalog of more than 500 molecular biology databases at INFOBIOGEN, France )
NAR 31 (1) 2003 (Nucl. Acids Res. biological database issue, papers available through NAR online)
NAR 32 (1) 2004 (Nucl. Acids Res. biological database issue, papers available through NAR online)
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Text-based database search
ENTREZ (Integrated database search for nucleotides, proteins, genomes, structures, populations sets and literature at NCBI, USA)
SRS (Search EMBL, SWISS-PROT, TrEMBL, PIR, PDB, etc. at EBI, UK)
DBGET/LinkDB (Integrated database search of LinkDB at GenomeNet, Kyoto University and University of Tokyo)
SSS (Sequence and structure searching site at Berkeley, US)
Molecules R US (Full text search of the PDB database at NIH)
MIA (Molecular Information Agent searching biological databases to find the existing information about a macromolecule at SDSC, USA)
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Sequence-based database search (sequence similarity search)
BLAST (Basic local alignment search tool at NCBI, USA)
FASTA (Fasta or fastx search at EBI, UK)
MPsrch (Smith-Waterman algorithm-based search at EBI, UK)
BLAST Microbial Genomes (Search finished and unfinished genomic sequences at NCBI)
Genome and proteome FASTA (at EBI, UK)
PIR-NRL3D (Sequence-structure data base search at John Hopkins University, USA)
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<strong>Motif-based database search
Kangaroo (Find sequences matching a given DNA or protein pattern at Mount Sinai Hospital, Toronto, Canada)
ScanProsite (Find protein sequences matching PROSITE or other patterns at ExPASy, CH)
ShapeSifter (Find protein sequences matching EMOTIF patterns at Stanford University, USA)
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Structure-based database search (structure similarity search)
Search_SCOP (Protein structure similarity search in SCOP database)
VAST (Structure-structure similarity search at NCBI, US)
DALI (Protein structure comparison with PDB at EBI,UK)
Finding 3D Similarity by CE (Combinatorial Extension) or CT (Compound Likeness) method at SDSC, USA)
LIBRA (Search sequences homologous to a given structure by Inverse Folding Protocol at NIG, Jp)
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Mass-based protein search
ProteinProspector (Proteomics tools for mining sequence databases in conjunction with mass spectrometry at UCSF, USA)
PeptIdent (Protein identification using pI, Mw and peptide mass fingerprinting data at ExPaSy, CH)
Prowl (Resource for protein chemistry and mass spectrometry at the Rockefeller University NY, USA)
Mascot (Protein identification using mass spectrometry data by Matrix Science, London, UK)
MassSearch (Search SwissProt or EMBL by protein mass after digestion at ETH Zurich, CH)
Mowse (Search the owl protein sequence database with protein fragment information at the HGMP-RC, UK)
PeptideSearch (Protein identification by peptide mapping or peptide sequencing at the EMBL, Heidelberg, Germany)
Lutefisk (Software for the de novo interpretation of peptide CID spectra from Immunex, Seattle, USA)
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DNA sequence analysis tools
Restriction; Detect repeats and unusual patterns
Restrictionmapper
Webcutter (Restriction analysis)
RepeatMasker (Search interspersed repeats and low complexity sequences)
REPuter (Fast computation of maximal repeats in complete genomes at Bielefeld University, Germany)
dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
Align (Pairwise sequence alignment with GAP, SIM Align sequences(DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
MAP (Multiple alignment of (long) sequences without penalizing large gaps)
ClustalW (at EBI, UK)
Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
Find genes
Sixframe (Translate DNA sequence in all 6 possible frames at Baylor College of Medecine, USA)
ORF Finder (at NCBI)
GeneMark (Species-specific search for genes at Georgia Institute of Technology , USA)
GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
GenLang (Exon recognition at University of Pennsylvania, USA).
GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
Find transcriptional elements
Identification of Prokaryotic/Eukaryotic Promoters (Promotor prediction in <100 kb DNA at Lawrence Berkeley National Laboratory, USA)
SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA)
FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA))
Find tRNA
tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, Fr)
Other tools
CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
MAR-Wiz (Search for matrix association regions at NCGR, Santa Fe, USA)
Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)
DNA folding server (Fold secondary structures)
PRIDE (Primer design at DFKZ, Heidelberg, Germany)
Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
PCR primer selection
Primer3 (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)
GeneFisher (Interactive PCR primer design tool at the University of Bielefeld, Germany)
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer design at the Weizmann Institute, Israel)
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RNA analysis tools
RNA Fold (Fold your own RNA sequences)
RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)
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Protein sequence and structure analysis tools
Physicochemical properties
ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
Analyse primary sequence
ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
SignalP (Prediction of peptide signal sequence at CBS, Denmark)
TargetP (Prediction of subcellular localization at CBS, Denmark)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
NetPhos (Prediction of phosphorylation sites in eukaryotic proteins at CBS, Denmark )
Scansite (Prediction of phosphorylation sites and protein binding sites at MIT, Cambridge, USA)
Helical Wheel (Representation of alpha-helical peptides)
Other primary sequence analysis tools at ExPaSy
Alignment
• Pairwise
Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
Pairwise sequence alignment (at Baylor College of Medecine, USA)
Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
• Multiple
ClustalW (at EBI, UK)
ClustalW (at the Baylor College of Medicine, USA)
MAP (Multiple alignment of (long) sequences without penalizing large gaps)
Multiple sequence alignment (at Baylor College of Medecine, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
Predict secondary structure
TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
SOSUI (Prediction of Transmembrane Regions, JP)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
PredictProtein (Protein secondary structure prediction at EMBL)
JPred (Protein secondary structure prediction at Dundee University, UK)
HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
PSIpred (Protein secondary structure prediction at Brunel University, UK)
nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
Other secondary structure prediction tools at ExPASy
BTPRED (Prediction of beta-turns at UCL, UK)
Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
PairCoil (Prediction of coiled Coil regions by Berger's method)
MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)
TOPS (Protein topology cartoon generation at University of Leeds, UK)
Analyse and model 3D structure
• 3D viewers
RasMol (Free offline 3D viewer. Download)
Swiss-Pdb Viewer (Deep View) (Free offline 3D viewing and analysis application, tightly linked to Swiss-Model. Tutorial)
Chime (Browser plugin for structure view from MDL Chemscape)
Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)
WebMol (Online 3D viewer at University of California, USA)
3D analysis
TOPS (Protein topology cartoon generation at University of Leeds, UK)
DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
OCA (Structure database browser at EBI, UK)
STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)
PsiPred (Sequence profile based fold recognition at Brunel University, UK)
Predicting Protein 3D structure based on homologous sequence search (EMBL Heidelberg, Germany)
123 (Fold prediction by aligning (threading) to a (set of) structure(s)
LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
CE (3-D protein structure comparison and alignment using the combinatorial extension (CE) method at SDSC, USA)
DALI (Automated Protein Structure Alignment at EBI,UK)
LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
VAST (Structure-structure similarity search at NCBI, US)
ASC (Analytic Surface Calculation of PDB molecules at IMP, Vienna)
MolSurfer (Calculate and navigate protein-protein interfaces at EML, Germany)
Protein-Protein Interaction Server (UCL, UK)
3D homology modeling
CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)
Swiss-Model (Automated protein homology-modeling server at ExPASy, Switzerland)
3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
FAMS (Fully Automated Modeling Service at Kitasato University, JP)
3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
SDSC1 (Protein structure homology modeling server at SDSC, USA)
Meta PP (Collection of structure prediction services at Columbia University, USA)
List of comparative modeling tools (at the Rockefeller University, NY, USA)
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Tools for protein function assignment
Scan or search for patterns, motifs, profiles, domains, families
ScanProsite (Scan a protein sequence against PROSITE pattern database at ExPASy, CH)
PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
PFSCAN (Scan protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)
BLOCKS Search (Scan a protein against BLOCKS database; also searches PRINTS)
eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies at Stanford University, USA)
Scansite (Prediction of protein signaling sequence motifs at MIT, Cambridge, USA)
MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
eMotif-maker (Build motifs that describe protein families or superfamilies at Stanford University, USA)
Meta-MEME (Buid motif at San Diego Supercomputer Centre, SDSC, Ca, USA)
CDART (Conserved Domain Architecture Retrieval Tool at NCBI, USA)
SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST at NCBI, USA)
COGnitor (Search a protein agains the COG database at NCBI)
iProClass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
ConSurf (Identification of functional regions in proteins by surface-mapping of phylogenetic information at Tel Aviv University, Israel)
ProDom (Automatically generated protein domain database at Toulouse, Fr)
Modules (Mobile protein domains database at EMBL)
SBASE (Protein domain library at ICGEB, Trieste, It)
HSSP (Database of homology-derived structures and sequences of proteins at EBI)
3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Chime plugin))
eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
GeneQuiz (Automated analysis of protein sequences at EMBL)
Search, computation and analysis of pathways
KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
aMAZE (Query tools for metabolic and signal transduction pathway analysis at ULB, Belgium)
Protein-protein interactionsDIP (Search Database of Interacting Proteins at UCLA, USA)
PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Canada)
BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Canada )
BINDBLAST (Search BIND database with BLAST)
MINT (Molecular INTeraction database at Rome University, It)
GRID (General Repository of Interaction Datasets at the Samuel Lunenfeld Research Institute, Canada)
PPI viewer (Mammalian protein-protein interaction database and viewer at RIKEN, Japan)
STRING (database of predicted functional associations among genes/proteins at the EMBL)
InterPrets (Interaction prediction through structure at the EMBL)
Protein Annotation
PAA (Protein Annotator's Assistant at EBI, UK)
AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Institute, UK)
Gene Ontology tools (Universal function annotation vocabulary by the Gene Ontology Consortium )
Automatic alert for related new sequence
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
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Phylogenetic Analysis
Multiple sequence alignment
ClustalW (Multiple sequence alignment at EBI, UK)
Multiple sequence alignment (at Baylor College of Medecine, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
Entrez-PopSet (Search set of DNA sequences from populations of related individuals/organisms at NCBI)
ConSurf (Identification of functional regions in proteins by surface-mapping of fhylogenetic information at Tel Aviv University, Israel)
Links to phylogeny software tools and servers (at the University of Washington, USA)
Organism classification
NCBI Taxonomy
The Tree of Life Project
TreeBASE (database of phylogenetic knowledge hosted by the University at Buffalo, USA)
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Microarray Data Browsing and Analysis
ArrayExpress (Repository for microarray data at EBI, UK)
GEO (Gene Exprssion Omnibus at NCBI)
SMD (Stanford microarray database, including microarray tools and tool links)
YMD (Yale microarray database)
Expression Profiler (Web-based microarray data analysis at EBI, UK)
GenMapp (Free computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes )
TBI Expression Analysis (Find differential genes between two filter hybridisation experiments at DFKZ, Heidelberg)
Other links to public microarray and gene expression databases
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Literature search
PubMed (Search public version of full Medline integrated in ENTREZ at NCBI, USA)
PubMed Central (Free online access to full text of life Science rechearch articles at NCBI, USA)
FreeMedicalJournals (Links to free online medical journals)
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
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Patent search
esp@cenet (Search for National and worldwide patents at European Patent Office)
USPTO (Search for US patents at US Patent and Trademark office)
DPD (DNA Patent Database at Georgetown University, US)
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Bioinformatics centers and servers
ANGIS (Australian National Genomic Information Service)
BEN (Belgian EMBNet Node)
Brutlag Bioinformatics Group (at Stanford University, USA)
CBS (Center for Biological Sequence analysis, Denmark)
CIB (Center for Information Biology, Mishima, Jp)
EBI (European Bioinformatics Institute, Hinxton, UK)
EMBnet and related WWW servers
ExPASy (Geneva, CH)
Genestream (at IGH, Montpellier, Fr)
GenomeNet Japan
ISCB (International Society for Computational Biology)
ISREC (Swiss Institute for Experimental Cancer Research)
MBCR (Biomedical Computing Facility)
MIPS (Munich Information Centre for Protein Sequences, Munich, Germ.)
NCBI (National Center for Biotechnology Information, Bethesda MD, USA)
NCGR (National Center for Genome Resources, Santa Fe, New Mexico, USA)
RFCGR (MRC Rosalind Franklin Centre for Genomic Research, Hinxton, UK)
Roslin Institute Bioinformatics (Edinburg, UK)
Sanger Institute (Hinxton, UK)SBG (Structural Bioinformatics Group at the EMBL, Heidelberg, Germany)
SDSC (San Diego Supercomputer Center, USA)
SHGC (Stanford Human Genome Center)
SIB (Swiss Institute for Bioinformatics, Geneva, CH)
Stanford Genome Technology Center
Stanford Genomic Resources
TIGR (The Institute for Genomic Research, USA)
UCL Biochemistry BSM Group (Biomolecular Structure and Modelling Group, UK)
Washington Genome Sequencing Center
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Links to other collections of bioinformatics resources
BioBencHelper
BIW (BioInformatics Web of Suresh Kumar)
BCM Search Launcher (Interface for related WWW tools at Baylor College of Medicine)
GenomeWeb (at the MRC RFCGR, Hinxton, UK)
HNB (Helmholz Network Network for Bioinformatics, Germany)
Luke's EMBOSS GUI (GUIs to EMBOSS, the European Molecular Biology Open Software Suite for sequence analysis)
AMOS' WWW Page Links (more than 1000 links listed by Amos Bairoch)
ExPASy Proteomics Tools (CH)
CMS Molecular Biology Resource (at San Diego Supercomupter Center, US)
Pack of WWW Tools for Molecular Analysis (at Adelaide University, Australia)
ABIM online Analysis Tools (Université Aix-Marseille, Fr)
Bioinformatics resources CCP11 (MRC, UK)
MolBiol.net (Links directory of bioinformatics, genomics, proteomics, biotechnology and molecular biology )
List of other Molecular Biology Resources
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Medical resources
OMIA (Online Mendelian Inheritance in Animals, University of Sydney, Australia)
OMIM (Online Mendelian Inheritance in Man at the NCBI)
The MERCK Manual of Diagnosis and Therapy (Guide to clinical information)
--------------------------------------------------------------------------------
Protocols
Protocol Online (Find/submit protocols in molecular biology, cell biology, immunology etc.)
Molecular Biology Protocols (collections of protocols)
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Software
BioCatalog (Software directory of general interest in molecular biology and genetics at EBI, UK)
Logiciels (Software directory at Institut Pasteur with links to providers and tutorials)
Molscript
NCBI Toolbox (NCBI software tools for building bioinformatics resources)
Phylogeny Programs (Collection of phylogeny software and servers)
BioPerl (international association of developers of open source Perl tools for bioinformatics, genomics and life science research)
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(Bio)chemistry
NIST Standard Reference Data Products Catalog
ChemFinder
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Educational resources
S-Star.org (Online Bioinformatics education by a collaboration of 7 universities wordwide)
BioComputing Hypertext Coursebook (Bielefeld, Germany)
Guide to Molecular Sequence Analysis (By Andrew Louka, University of Oslo, Norway)
NCBI Education (Bioinformatics definitions and tutorials at the NCBI, USA)
Molecules in the Classroom (UMass Amherst USA)
DNA Structure
NDB Biomolecular Resource (Nucleic Acid education)
NDB Atlas of Nucleic Acid Containing Structures
Teachers' Molecular Visualization Resources
BioMolecular Structure Education Web Sites
Biochemistry in 3d (Accompanies Lehninger Principles of Biochemistry)
IMAGE (Image library of biological macromolecules from IMB Jena Biocomputing Group, Jena, Germ.)
Protein Crystallography on the Web (University of London, UK)
Genious software
Winappz Geneious Pro v4.8.3 32.9 MBGeneious combines all the leading DNA and protein sequence analysis tools into one revolutionary software solution! Its ease of use makes bioinformatics accessible to any biologist.
It runs on all major operating systems and is very affordable. Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more. It even includes an API for creating your own plugins.Popular Geneious Pro use casesHere are just some examples of everyday research work that Geneious Pro can do for you.Sequence Analysis:Pairwise and multiple sequence alignment including ClustalW, MUSCLE, Progressive pairwise and translation alignmentPhylogenetic tree building with NJ, bootstrapping, consensus trees and plugins for PAUP* and MrBayesConsensus sequence, translation, complement and protein statistics update as you editFind motifs, open reading frames (ORFs)Lab End Sequence Analysis:Contig assembly with automated trimming, vector screening, assembly, and chromatogram editing454 import and reference assembly with support for viewing large assembliesRestriction and Gateway® Cloning, restriction mapping, digestion and ligationAutomated primer design with degeneracy supportKeep a primer database and search for primers which match new sequences.Sequence Visualization:Customizable graphical viewer and editor of sequences, alignments and annotationsFully interactive, customizable plasmid mapsNavigate chromosomes and genomesPhylogenetic tree viewer with customizable layout, color and styleGraphs updated real-time including sequence logos, chromatogram traces and protein properties3D protein structure viewingFast, interactive dot plotsEasy image export to publication quality formats and More…Organize and share data:Store and organize all of your research material in one place including sequences, publications, trees and moreExtensive import and export including Vector NTI, Nexus, GenBank, Fasta, PDF, ABI and many more!Collaborate and share data over the internet or on a secure, central server.Search and sort sequences by similarity, basic and advanced text searching of dataAttach structured information to sequences, alignments and trees.Access public databases:Drag and drop sequences from NCBI (including Gene, Genome, Nucleotide, SNP, Structure and Protein)NCBI BLAST sequences with two clicks of the mouseKeeps your NCBI and EMBL downloads up to date automaticallyClose integration with Pfam databasesA unique method of rapidly filtering public data as it downloads.Teach Bioinformatics:Create interactive tutorials with direct links to material in GeneiousAll the tools a budding bioinformatician may need is just a click awayStudents can answer question, do analyses then submit their results using Collaboration.Manage references:Automatically retrieves newly published articles from PubMed and can sort them based on your interestsStorage of abstracts and bibliographic informationQuick links to find original articles and citation record online.Downloadhttp://hotfile.com/dl/21128736/f84d0ed/Geneious.Pro.v4.8.3.Incl.Keygen.and.Patch-iNViSiBLE.rar.html
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