Jant's web site

Rosetta docking server
GRAMM
AutoDock
Bielefeld Protein Docking.
DOCK
DOT
FTDock, RPScore and MultiDock.
Hex 3.0
ICM Protein-Protein docking
KORDO
Nussinov-Wolfson Structural Bioinformatics Group.
ZDOCK rigid-body protein-protein docking software, using a Fast Fourier Transform search algorithm.
RDOCK a refinement method to minimize energy and re-rank ZDOCK predictions.
Docking Benchmark a large set of test cases for evaluating the performance of docking algorithms.
ZDOCK Conv3D ZDOCK optimized with a new convolution library, resulting in improved speed and less memory usage.
ZDOCK Server an automated server for running ZDOCK, with capabilities for blocking and filtering contact residues.

Databases and Web servers for structure-based analysis of biological molecules

ADAN
3DID
CAPRI
GRAMM-X
InterPreTS
Intervor
PIbase
PQS
PISA
PITA
PP
ProtBuD

ASEdb
ClusPro
ConSurf
Interpro
Ipfam
MultiDock
PRISM
ProFace
RosettaDock
SCOP
Scorecons
3DComplex

Dockground
ExPASy
Protein Lysine Modification Database
HADDOCK
PatchDock
PiQSi
PFAM
SKE-Dock
SmoothDock
SymmDock
VIPERdb
PDBsum

Identification and characterization with peptide mass fingerprinting data.

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

Mascot - Peptide mass fingerprint from Matrix Science Ltd., London

PepMAPPER - Peptide mass fingerprinting tool from UMIST, UK

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

QuickMod - Open modification spectral library search tool for identification of MS/MS data

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

ProteinProspector - UCSF tools for fragment-ion masses data (MS-Tag, MS-Seq, MS-Product, etc.)

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

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

xComb - computes all possible crosslinks based on proteins of interest for further interrogation using standard search engine

xQuest - Search machine to identify cross-linked peptides from complex samples and large protein sequence databases

SmileMS - Small molecule identification

SmileMS molecule toolkit - isotopes pattern calculator, mass to formula, mass to pubchem compounds

Glycotools

GlycanMass - Calculate the mass of an oligosaccharide structure

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)

GlycospectrumScan - an analytical tool independent of MS-platform that accurately identifies and assigns the oligosaccharide heterogeneity on glycopeptides from MS data of a mixture of peptides and glycopeptides (Reference)

Glycoviewer - a visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG) (Reference)

Other tools for MS data (vizualisation, quantitation, analysis, etc.)

HCD/CID spectra merger - a tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines

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

Other tools for 2-DE data (image analysis, data publishing, etc.)

ImageMaster / Melanie - Software for 2-D PAGE analysis

Make2D-DB II - A package to build a web-based proteomics database

DNA - 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

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

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

BLAST2FASTA - Converts NCBI BLAST output into FASTA format

Pattern and profile searches

InterPro Scan - Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases

MyHits - 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]

ProDom - Compares sequences with ProDom search utility

SUPERFAMILY Sequence Search - Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models

FingerPRINTScan - Scans a protein sequence against the PRINTS Protein Fingerprint Database

3of5 - Complex Pattern Search - e.g. to search for a motif with 3 basic AA in 5 positions

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

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

GPS - Prediction of kinase-specific phosphorylation sites for 408 human protein kinases in hierarchy

Sulfinator - Prediction of tyrosine sulfation sites

SulfoSite - Prediction of tyrosine sulfation sites

SUMOplot - Prediction of SUMO protein attachment sites

SUMOsp - Prediction of sumoylation 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)

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

MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve

Scratch Protein Predictor

HeliQuest - A web server to screen sequences with specific alpha-helical properties

Radar - De novo repeat detection in protein sequences

REP - Searches a protein sequence for repeats

REPRO - De novo repeat detection in protein sequences

T-REKS - De novo detection and alignment of repeats 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 probabilities with the Paircoil algorithm.

Multicoil - Prediction of two- and three-stranded coiled coils

2ZIP - Prediction of Leucine Zippers

ePESTfind - Identification of PEST regions

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

PepDraw - peptide primary structure drawing

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

CFSSP - Chou & Fasman 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)

NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions

NetTurnP - Prediction of Beta-turn regions in protein sequences

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 Bloomsbury Centre for Bioinformatics

SOPMA - Geourjon and Delage, 1995

Scratch Protein Predictor

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 (currently down)

MolTalk - A computational environment for structural bioinformatics

COPS - Navigation through fold space and the instantaneous visualization of pairwise structure similarities

PoPMuSiC - Prediction of thermodynamic stability changes upon point mutations; design of modified proteins

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 - Homology modeling

SWISS-MODEL - An automated knowledge-based protein modelling server

CPHmodels - Automated neural-network based protein modelling server

ESyPred3D - Automated homology modeling program using neural networks

Geno3d - Automatic modelling of protein three-dimensional structure

Threading

Phyre (Successor of 3D-PSSM) - Automated 3D model building using profile-profile matching and secondary structure

Fugue - Sequence-structure homology recognition

HHpred - Protein homology detection and structure prediction by HMM-HMM comparison

LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment

SAM-T08 - HMM-based Protein Structure Prediction

PSIpred - Various protein structure prediction methods (including threading) at Bloomsbury Centre for Bioinformatics

Ab initio

HMMSTR/Rosetta - Prediction of protein structure from sequence

Assessing tertiary structure prediction

Anolea - Atomic Non-Local Environment Assessment

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

QMEAN - Server for Model Quality Estimation

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

Molecular modeling and visualization tools

Swiss-PdbViewer - A program to display, analyse and superimpose protein 3D structures

SwissDock - Docking of small ligands into protein active sites with EADock DSS

SwissParam - Topology and parameters for small molecules, for use with CHARMM and GROMAC

Ascalaph Packages

Astex Viewer

Jmol

MarvinSpace - 3D molecule visualization tool

MolMol

MovieMaker - For rapid rendering of protein motions and interactions

PyMol

Rasmol

SRS 3D

VMD

YASARA - Molecular graphics, modeling, simulations and eLearning

Prediction of disordered regions

DisEMBL - Protein disorder prediction

GlobPlot - Protein disorder/order/globularity/domain predictor

MeDor - Metaserver or Disorder

POODLE - Prediction Of Order and Disorder by machine LEarning

List of Protein Disorder Predictors

Sequence alignment

Binary

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

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 Vital-IT , 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 GenoToul Bioinfo 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)

Phylogenetic analysis

BIONJ - Server for NJ phylogenetic analysis

DendroUPGMA

PHYLIP - Server for phylogenetic analysis using the PHYLIP package

PhyML - Server for ML phylogenetic analysis

Phylogeny.fr - Robust Phylogenetic Analysis For The Non-Specialist

The PhylOgenetic Web Repeater (POWER) - Performs phylogenetic analysis

BlastO - Blast on orthologous groups

Evolutionary Trace Server (TraceSuite II) - Maps evolutionary traces to structures

Phylogenetic programs - List of phylogenetic packages and free servers (PHYLIP pages)

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

Medline Ranker

The Miner Suite - of bioinformatic software packages and data analysis

XplorMed - Explore a set of abstracts derived from a bibliographic search in MEDLINE

Statistical tools

pROC - A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves)

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