Bioinformatic tools and Molecular Modeling Software

DNA: [DNA to Protein]

Proteins: [Similarity searches] [Pattern and profile searches] [Post-translational modification prediction] [Topology prediction] [Primary structure analysis] [Secondary structure prediction] [Tertiary structure] [Sequence alignment][Gateways] [Phylogenetic analysis] [Biological text analysis]

Modeling: [Molecular Modeling and visualization tools]

Proteomic:[Protein identification and characterization] [Other proteomics tools]

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DNA to Protein
Translate - Translates a nucleotide sequence to a protein sequence Transeq - Nucleotide to protein translation from the EMBOSS package Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner BCM search launcher - Six frame translation of nucleotide sequence(s) Reverse Translate - Translates a protein sequence back to a nucleotide sequence (Reverse)-Transcription and Translation Tool Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters List of gene identification software sites Similarity searches BLAST Network Service on ExPASy BLAST at EMBnet-CH/SIB (Switzerland) BLAST at NCBI WU-BLAST at Bork's group in EMBL (Heidelberg) WU-BLAST and BLAST at the EBI (Hinxton) BLAST at PBIL (Lyon) Fasta3 - FASTA version 3 at the EBI FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH MPsrch - Smith/Waterman sequence comparison at EBI PropSearch - Structural homolog search using a 'properties' approach at Montpellier SAMBA - Systolic Accelerator for Molecular Biological Applications SAWTED - Structure Assignment With Text Description Scanps - Similarity searches using Barton's algorithm SEQUEROME - BLAST similarity search and sequence profiling at Georgetown University SHOPS - Analysis of the genomic operon context for any group of proteins

DNA to Protein

Translate - Translates a nucleotide sequence to a protein sequence
Transeq - Nucleotide to protein translation from the EMBOSS package
Graphical Codon Usage Analyser - Displays the codon bias in a graphical manner
BCM search launcher - Six frame translation of nucleotide sequence(s)
Reverse Translate - Translates a protein sequence back to a nucleotide sequence
(Reverse)-Transcription and Translation Tool
Genewise - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters
List of gene identification software sites

Similarity searches

BLAST Network Service on ExPASy
BLAST at EMBnet-CH/SIB (Switzerland)
BLAST at NCBI
WU-BLAST at Bork's group in EMBL (Heidelberg)
WU-BLAST and BLAST at the EBI (Hinxton)
BLAST at PBIL (Lyon)
Fasta3 - FASTA version 3 at the EBI
FDF - Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH
MPsrch - Smith/Waterman sequence comparison at EBI
PropSearch - Structural homolog search using a 'properties' approach at Montpellier
SAMBA - Systolic Accelerator for Molecular Biological Applications
SAWTED - Structure Assignment With Text Description
Scanps - Similarity searches using Barton's algorithm
SEQUEROME - BLAST similarity search and sequence profiling at Georgetown University
SHOPS - Analysis of the genomic operon context for any group of proteins

Pattern and profile searches
InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases Hits - Relationships between protein sequences and motifs ScanProsite - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL) HamapScan - Scans a sequence against the HAMAP families MotifScan - Scans a sequence against protein profile databases (including PROSITE) Pfam HMM search; scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre] FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database 3of5 - Complex Pattern Search ELM - Eukaryotic Linear Motif resource for functional sites in proteins PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ] PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL SMART - Simple Modular Architecture Research Tool; at EMBL TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM 9aaTAD - Prediction of Nine Amino Acid Transactivation Domain

Pattern and profile searches

InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases
Hits - Relationships between protein sequences and motifs
ScanProsite - Scans a sequence against PROSITE or a pattern against the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
HamapScan - Scans a sequence against the HAMAP families
MotifScan - Scans a sequence against protein profile databases (including PROSITE)
Pfam HMM search; scans a sequence against the Pfam protein families db [At Washington University or at Sanger Centre]
FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database
3of5 - Complex Pattern Search
ELM - Eukaryotic Linear Motif resource for functional sites in proteins
PRATT - Interactively generates conserved patterns from a series of unaligned proteins; [at EBI / ExPASy ]
PPSEARCH - Scans a sequence against PROSITE (allows a graphical output); at EBI
PROSITE scan - Scans a sequence against PROSITE (allows mismatches); at PBIL
PATTINPROT - Scans a protein sequence or a protein database for one or several pattern(s); at PBIL
SMART - Simple Modular Architecture Research Tool; at EMBL
TEIRESIAS - Generate patterns from a collection of unaligned protein or DNA sequences; at IBM
9aaTAD - Prediction of Nine Amino Acid Transactivation Domain

Post-translational modification prediction
ChloroP - Prediction of chloroplast transit peptides LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria MITOPROT - Prediction of mitochondrial targeting sequences PATS - Prediction of apicoplast targeted sequences PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum Predotar - Prediction of mitochondrial and plastid targeting sequences PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins SignalP - Prediction of signal peptide cleavage sites DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium NetCGlyc - C-mannosylation sites in mammalian proteins NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins NetGlycate - Glycation of epsilon amino groups of lysines in mammalian proteins NetNGlyc - Prediction of N-glycosylation sites in human proteins OGPET - Prediction of O-GalNAc (mucin-type) glycosylation sites in eukaryotic (non-protozoan) proteins YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences big-PI Predictor - GPI Modification Site Prediction DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site) GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map Myristoylator - Prediction of N-terminal myristoylation by neural networks NMT - Prediction of N-terminal N-myristoylation CSS-Palm - Palmitoylation site prediction with CSS PrePS - Prenylation Prediction Suite NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins) NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins NetPhosK - Kinase specific phosphorylation sites in eukaryotic proteins NetPhosYeast - Serine and threonine phosphorylation sites in yeast proteins Sulfinator - Prediction of tyrosine sulfation sites SulfoSite - Prediction of tyrosine sulfation sites SUMOplot - Prediction of SUMO protein attachment sites TermiNator - Prediction of N-terminal modification (version 3) NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins NetCorona - Coronavirus 3C-like proteinase cleavage sites in proteins ProP - Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences

Post-translational modification prediction

ChloroP - Prediction of chloroplast transit peptides
LipoP - Prediction of lipoproteins and signal peptides in Gram negative bacteria
MITOPROT - Prediction of mitochondrial targeting sequences
PATS - Prediction of apicoplast targeted sequences
PlasMit - Prediction of mitochondrial transit peptides in Plasmodium falciparum
Predotar - Prediction of mitochondrial and plastid targeting sequences
PTS1 - Prediction of peroxisomal targeting signal 1 containing proteins
SignalP - Prediction of signal peptide cleavage sites
DictyOGlyc - Prediction of GlcNAc O-glycosylation sites in Dictyostelium
NetCGlyc - C-mannosylation sites in mammalian proteins
NetOGlyc - Prediction of O-GalNAc (mucin type) glycosylation sites in mammalian proteins
NetGlycate - Glycation of epsilon amino groups of lysines in mammalian proteins
NetNGlyc - Prediction of N-glycosylation sites in human proteins
OGPET - Prediction of O-GalNAc (mucin-type) glycosylation sites in eukaryotic (non-protozoan) proteins
YinOYang - O-beta-GlcNAc attachment sites in eukaryotic protein sequences
big-PI Predictor - GPI Modification Site Prediction
DGPI - Prediction of GPI-anchor and cleavage sites (Mirror site)
GPI-SOM - Identification of GPI-anchor signals by a Kohonen Self Organizing Map
Myristoylator - Prediction of N-terminal myristoylation by neural networks
NMT - Prediction of N-terminal N-myristoylation
CSS-Palm - Palmitoylation site prediction with CSS
PrePS - Prenylation Prediction Suite
NetAcet - Prediction of N-acetyltransferase A (NatA) substrates (in yeast and mammalian proteins)
NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
NetPhosK - Kinase specific phosphorylation sites in eukaryotic proteins
NetPhosYeast - Serine and threonine phosphorylation sites in yeast proteins
Sulfinator - Prediction of tyrosine sulfation sites
SulfoSite - Prediction of tyrosine sulfation sites
SUMOplot - Prediction of SUMO protein attachment sites
TermiNator - Prediction of N-terminal modification (version 3)
NetPicoRNA - Prediction of protease cleavage sites in picornaviral proteins
NetCorona - Coronavirus 3C-like proteinase cleavage sites in proteins
ProP - Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences

Topology prediction
NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins PSORT - Prediction of protein subcellular localization SecretomeP - Non-classical and leaderless secretion of proteins TargetP - Prediction of subcellular location TatP - Twin-arginine signal peptides DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) PredictProtein - Prediction of transmembrane helix location and topology (Columbia University) SOSUI - Prediction of transmembrane regions (Nagoya University, Japan) TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden) TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark) TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH) TopPred - Topology prediction of membrane proteins (France)

Topology prediction

NetNES Leucine-rich nuclear export signals (NES) in eukaryotic proteins
PSORT - Prediction of protein subcellular localization
SecretomeP - Non-classical and leaderless secretion of proteins
TargetP - Prediction of subcellular location
TatP - Twin-arginine signal peptides
DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)
HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)
PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)
SOSUI - Prediction of transmembrane regions (Nagoya University, Japan)
TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
TopPred - Topology prediction of membrane proteins (France)

Primary structure analysis
ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.) Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states Jena-Library - Jena Library of Biological Molecules. The amino Acid Repository* MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve Radar - De novo repeat detection in protein sequences REP - Searches a protein sequence for repeats REPRO - De novo repeat detection in protein sequences TRUST - De novo repeat detection in protein sequences XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI] Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL] Paircoil - Prediction of coiled coil regions in proteins (Berger's method) Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm. Multicoil - Prediction of two- and three-stranded coiled coils 2ZIP - Prediction of Leucine Zippers PESTfind - Identification of PEST regions at EMBnet Austria HLA_Bind - Prediction of MHC type I (HLA) peptide binding PEPVAC - Prediction of supertypic MHC binders RANKPEP - Prediction of peptide MHC binding SYFPEITHI - Prediction of MHC type I and II peptide binding ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.) Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence Peptide Builder Protein Colourer - Tool for coloring your amino acid sequence Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa Three-/one-letter amino acid converter - tool which converts amino acid codes from three-letter to one-letter and vice versa. Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel RandSeq - Random protein sequence generator

Primary structure analysis

ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
ScanSite pI/Mw - Compute the theoretical pI and Mw, and multiple phosphorylation states
Jena-Library - Jena Library of Biological Molecules. The amino Acid Repository*
MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve
Radar - De novo repeat detection in protein sequences
REP - Searches a protein sequence for repeats
REPRO - De novo repeat detection in protein sequences
TRUST - De novo repeat detection in protein sequences
XSTREAM - De novo tandem repeat detection and architecture modeling in protein sequences
SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]
Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]
Paircoil - Prediction of coiled coil regions in proteins (Berger's method)
Paircoil2 - Prediction of the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm.
Multicoil - Prediction of two- and three-stranded coiled coils
2ZIP - Prediction of Leucine Zippers
PESTfind - Identification of PEST regions at EMBnet Austria
HLA_Bind - Prediction of MHC type I (HLA) peptide binding
PEPVAC - Prediction of supertypic MHC binders
RANKPEP - Prediction of peptide MHC binding
SYFPEITHI - Prediction of MHC type I and II peptide binding
ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
Peptide Builder
Protein Colourer - Tool for coloring your amino acid sequence
Three To One and One to Three - Tools to convert a three-letter coded amino acid sequence to single letter code and vice versa
Three-/one-letter amino acid converter - tool which converts amino acid codes from three-letter to one-letter and vice versa.
Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel
RandSeq - Random protein sequence generator

Secondary structure prediction
AGADIR - An algorithm to predict the helical content of peptides APSSP - Advanced Protein Secondary Structure Prediction Server GOR - Garnier et al, 1996 HNN - Hierarchical Neural Network method (Guermeur, 1997) HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction Jpred - A consensus method for protein secondary structure prediction at University of Dundee JUFO - Protein secondary structure prediction from sequence (neural network) nnPredict - University of California at San Francisco (UCSF) Porter - University College Dublin PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction PSA - BioMolecular Engineering Research Center (BMERC) / Boston PSIpred - Various protein structure prediction methods at Brunel University SOPMA - Geourjon and Deléage, 1995 SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology

Secondary structure prediction

AGADIR - An algorithm to predict the helical content of peptides
APSSP - Advanced Protein Secondary Structure Prediction Server
GOR - Garnier et al, 1996
HNN - Hierarchical Neural Network method (Guermeur, 1997)
HTMSRAP - Helical TransMembrane Segment Rotational Angle Prediction
Jpred - A consensus method for protein secondary structure prediction at University of Dundee
JUFO - Protein secondary structure prediction from sequence (neural network)
nnPredict - University of California at San Francisco (UCSF)
Porter - University College Dublin
PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University
Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction
PSA - BioMolecular Engineering Research Center (BMERC) / Boston
PSIpred - Various protein structure prediction methods at Brunel University
SOPMA - Geourjon and Deléage, 1995
SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California
DLP-SVM - Domain linker prediction using SVM at Tokyo University of Agriculture and Technology

Tertiary structure
Tertiary structure analysis
iMolTalk - An Interactive Protein Structure Analysis Server MolTalk - A computational environment for structural bioinformatics qCOPS - navigation through fold space and the instantaneous visualization of pairwise structure similarities Seq2Struct - A web resource for the identification of sequence-structure links STRAP - A structural alignment program for proteins TLSMD - TLS (Translation/Libration/Screw) Motion Determination TopMatch-web - protein structure comparison
Tertiary structure prediction
Comparative modeling SWISS-MODEL - An automated knowledge-based protein modelling server 3Djigsaw - Three-dimensional models for proteins based on homologues of known structure CPHmodels - Automated neural-network based protein modelling server ESyPred3D - Automated homology modeling program using neural networks Geno3d - Automatic modelling of protein three-dimensional structure SDSC1 - Protein Structure Homology Modeling Server Threading 3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit) Fugue - Sequence-structure homology recognition HHpred - Protein homology detection and structure prediction by HMM-HMM comparison Libellula - Neural network approach to evaluate fold recognition results LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment SAM-T08 - HMM-based Protein Structure Prediction Threader - Protein fold recognition ProSup - Protein structure superimposition SWEET - Constructing 3D models of saccharides from their sequences Ab initio HMMSTR/Rosetta - Prediction of protein structure from sequence
Assessing tertiary structure prediction
Anolea - Atomic Non-Local Environment Assessment Biotech Validation Suite for Protein Structures EVA - EValuation of Automatic protein structure prediction LiveBench - Continuous Benchmarking of Structure Prediction Servers NQ-Flipper - validation and correction of asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography PROCHECK - Verification of the stereochemical quality of a protein structure ProSA-web - recognition of errors in 3D structures of proteins What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics
Quaternary structure
MakeMultimer - reconstruction of multimeric molecules present in crystals EBI PISA - Protein Interfaces, Surfaces and Assemblies PQS - Protein Quaternary Structure Query form at the EBI ProtBud - comparison of asymmetric units and biological units from PDB and PQS


Prediction of disordered regions
DisEMBL - Protein disorder prediction GlobPlot - Protein disorder/order/globularity/domain predictor List of Protein Disorder Predictors

Sequence alignment
Binary
SIM + LALNVIEW - Alignment of two protein sequences with SIM, results can be viewed with LALNVIEW LALIGN - Finds multiple matching subsegments in two sequences Dotlet - A Java applet for sequence comparisons using the dot matrix method
Multiple
Decrease redundancy - Reduce a set of sequences into a non-redundant set Nomad (Neighborhood Optimization for Multiple Alignment Discovery) - Ungapped local multiple alignment, optimized for protein sequences, even when distantly related CLUSTALW [At EBI, PBIL, My Hits or at EMBnet-CH] KALIGN - an accurate and fast multiple sequence alignment algorithm [At Karolinska Institute or at EBI] MAFFT [At Kyushu University, EBI or at MyHits] Muscle [At Berkeley or at BioAssist] T-Coffee [At MyHits, BioAssist or at EBI] MSA - at Genestream (IGH) DIALIGN - Multiple sequence alignment based on segment-to-segment comparison, at University of Bielefeld, Germany Match-Box - at University of Namur, Belgium - at Washington University Multalin [At INRA or at PBIL] MUSCA - Multiple sequence alignment using pattern discovery, at IBM
Alignment analysis
AMAS - Analyse Multiply Aligned Sequences Bork's alignment tools - Various tools to enhance the results of multiple alignments (including consensus building). CINEMA - Color Interactive Editor for multiple alignments ESPript - Tool to print a multiple alignment MaxAlign - Post-processing of alignments by removing sequences (taxa) with many gaps PhyloGibbs - Gibbs motif sampler incorporating phylogeny and tracking statistics SVA - Sequence Variability Analyser for multiple alignments PVS - a protein variability server optimized for conserved epitope discovery WebLogo - Sequence logos at Berkeley/USA plogo - Sequence logos at CBS/Denmark GENIO/logo - Sequence logos at Stuttgart/Germany SeqLogo - Sequence logos at the Immunomedicine Group, Facultad de Medicina, U.C.M, Spain (The Molecular Immunology Foundation (MIF) does not exist anymore)

Gateways
Biosyn Gizmo - bundle of databases (siRNA, protein, peptide antigen) and tools

Phylogenetic analysis
Phylogenetic programs - List of phylogenetic packages and free servers (PHYLIP pages) PHYLIP - Server for phylogenetic analysis using the PHYLIP package BIONJ - Server for NJ phylogenetic analysis Evolutionary Trace Server (TraceSuite II) - Maps evolutionary traces to structures

Biological text analysis

AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
BioMinT - Mining the biomedical literature
GPSDB - Gene and Protein Synonym DataBase
MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

Molecular modeling and visualization tools

Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures
Swiss-Model Workspace - Homology modeling server. An automated comparative protein Modelling Environment
Ascalaph Packages
Astex Viewer
Jmol
MolMol
MovieMaker - For rapid rendering of protein motions and interactions
PyMol - Edition and visualization tool of high quality*
Rasmol
VMD
YASARA - Molecular graphics, modeling, simulations and eLearning
NAMD - Molecular Dynamics. Energy minimization and equilibration in water*
CHARMM_GUI - Macromolecular dynamics and mechanism*

Docking programs

DOCK - Program for docking and Tutorial*
AUTODOCK - Program for docking inlcuding AutoDockTools
ZINC DATABASE - A drug database which is not commercial*
SEArch - Similarity Ensemble Approach*

Protein identification and characterization
Identification and characterization with peptide mass fingerprinting data
Aldente - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion. Download the stand-alone version FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest. FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides) Mascot - Peptide mass fingerprint from Matrix Science Ltd., London PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK PFMUTS - Shows the possible single and double mutations of a peptide fragment from MALDI peptide mass fingerprinting ProFound - Search known protein sequences with peptide mass information from Rockefeller and NY Universities [or from Genomic Solutions] ProteinProspector - UCSF tools for peptide masses data (MS-Fit, MS-Pattern, MS-Digest, etc.)
Identification and characterization with MS/MS data
Popitam - Identification and characterization tool for peptides with unexpected modifications (e.g. post-translational modifications or mutations) by tandem mass spectrometry Phenyx - Protein and peptide identification/characterization from MS/MS data from GeneBio, Switzerland Mascot - Sequence query and MS/MS ion search from Matrix Science Ltd., London OMSSA - MS/MS peptide spectra identification by searching libraries of known protein sequences PepFrag - Search known protein sequences with peptide fragment mass information from Rockefeller and NY Universities [or from Genomic Solutions] ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.) SearchXLinks - Analysis of mass spectra of modified, cross-linked, and digested proteins whose amino acid sequence is known, from Caesar, Germany
Identification with isoelectric point, molecular weight and/or amino acid composition
AACompIdent - Identify a protein by its amino acid composition AACompSim - Compare the amino acid composition of a UniProtKB/Swiss-Prot entry with all other entries TagIdent - Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw MultiIdent - Identify proteins with isoelectric point (pI), molecular weight (Mw), amino acid composition, sequence tag and peptide mass fingerprinting data
Other prediction or characterization tools
ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.) Compute pI/Mw - Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence GlycanMass - Calculate the mass of an oligosaccharide structure PeptideCutter - Predicts potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence PeptideMass - Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence IsotopIdent - Predicts the theoretical isotopic distribution of a peptide, protein, polynucleotide or chemical compound

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Other proteomics tools
Other tools for MS data (vizualisation, quantitation, analysis, etc.)
MALDIPepQuant - Quantify MALDI peptides (SILAC) from Phenyx output MSight - Mass Spectrometry Imager pIcarver - Visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies ImageMaster / Melanie - Software for 2-D PAGE analysis Make2D-DB II - A package to build a web-based proteomics database

Last Modified: 09 Jun 2009