Topology prediction

·         PSORT - Prediction of protein subcellular localization

·         TargetP - Prediction of subcellular location

·         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 (TUAT; Tokyo Univ. of Agriculture & Technology)

·         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 2 - Topology prediction of membrane proteins (Stockholm University)

Primary structure analysis

·         ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)

·         Compute pI/Mw - Compute the theoretical pI and Mw from a Swiss-Prot or TrEMBL entry or for a user sequence

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

·         REP - Searches a protein sequence for repeats

·         REPRO - De novo repeat detection in protein sequences

·         Radar - De novo repeat detection 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)

·         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

·         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

·         Protein Colourer - Tool for coloring your amino acid sequence

·         Three To One - Tool to convert a three-letter coded amino acid sequence to single letter code

·         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)

·         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)

·         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

Tertiary structure

Tertiary structure analysis

·         iMolTalk - An Interactive Protein Structure Analysis Server

·         MolTalk - A computational environment for structural bioinformatics

·         Seq2Struct - A web resource for the identification of sequence-structure links

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

·         Libellula - Neural network approach to evaluate fold recognition results

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

·         SAM-T02 - 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

·         PROCHECK - Verification of the stereochemical quality of a protein structure

·         What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics

Molecular modeling and visualization tools

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

·         Astex Viewer

·         MolMol

·         Rasmol

·         VMD

Prediction of disordered regions

·         DisEMBL - Protein disorder prediction

·         GlobPlot - Protein disorder/order/globularity/domain predictor