Protein Secondary Structure Prediction

QL - Quadratic-Logistic prediction method, based on maximum-likelihood methods (NIH only)
QL With Homologs - Quadratic-Logistic prediction method from multiple sequences (NIH only)
GOR-IV - from the Garnier group (NIH only)
SAM-T02 - HMM-based, by Kevin Karplus as UCSC
PSIPRED - Fast response, Based on neural networks and BLAST, at London's Global Univ.
PredictProtein - comprehensive sequence analysis and structure prediction
ProDom - protein domain family database, at CNRS, France
Pfam - multiple sequence alignments and hidden Markov models, The Sanger Institute
metaPrDOS - meta Protein DisOrder prediction System, at Univ. of Tokyo
EMBOSS-Lite - pepwheel - (equivalent to GCG Helicalwheel) at Helix Systems (NIH only)
Helical Wheel Applet - at University of Virginia
OCTOPUS - Prediction of membrane protein topology and signal peptides, at Stockholm University

Ab initio Protein Modelling

ROBETTA - Full-chain Protein Structure Prediction Server, very slow queuing system
PCONS - Protein Structure Prediction Meta Server, at Univ. of Stockholm

Comparative Protein Modelling

Swiss-Model - an automated comparative protein modelling server, at ExPASy.org
SCRWL server - builds homology models for molecular replacement, JCSG
M4T - fully automatic comparative modelling, Yale University
GeneSilico Metaserver - gateway to various protein structure prediction methods
BionInfoBank Meta Server - gateway to structural and functional prediction
nFOLD3 - generate 3D models of a protein from several profile-profile alignment methods, at Univ. of Reading
CPHmodels - homology modeling, at CBS Tech. Univ. of Denmark
3D-Jigsaw - homology modeling, at Cancer Researck UK
ESyPred3D - homology modeling, at Univ. of Namur, Belgium
(PS)² - homology modeling, at National Chiao Tung University
SAM-T08 - HMM-based secondary structure prediction and homology modeling, at UCSC
HOMODELLER - homology modeling, at Univ. of Alberta
I-TASSER - homology modeling using threading and simulation, at Univ. of Kansas

Protein Threading

PROSPECT - very fast parallelized version of PROSPECT v2.0, at Helix Systems (NIH only)
MUSTER - combines sequence profile-profile alignment with multiple structural information, at Univ. of Kansas
WURST - Protein threading web server, at Univ. of Hamburg
PHYRE - Protein Homology/analogY Recognition Engine, at Imperial College London
LOOPP@BioHPC - Learning, Observing and Outputting Protein Patterns, at Cornell Univ.

Other Protein Modelling

FRpred - Prediction of protein functional residues from sequence by probability density estimation, at MPIDB
BONGO - Structural effect prediction of non-synonymous SNPs, at Univ. of Cambridge
DISOclust - predicts protein disorder, at Univ. of Reading
RosettaDesign - predicts sequences that fit into structures, at Univ. North Carolina
Rosetta Antibody Server - predicts antibody structure for a given antigen, at Johns Hopkins Univ.
elNémo - Elastic Network Model, computes low frequency normal modes of a protein, at CNRS
OCTOPUS/SPOCTOPUS - prediction of membrane protein topology and signal peptides, at Stockholm Univ.
SitePredict - binding site prediction for metal ions or small molecules, at the Mayo Clinic
IUPred - links to servers for prediction of protein disorder, at Hungarian Acad. of Sciences
Zinc Finger Prediction - scores the probability of a zinc finger binding to target DNA, at Princeton Univ.

Protein Quaternary Structure Prediction

ClusPro - fully automatic protein-protein docking
NetworkBLAST - find evolutionarily conserved protein interaction networks, at Tel Aviv Univ.
NetMHC 3.0 - Predicts binding of peptides to HLA alleles, at Tech. Univ. of Denmark
HADDOCK - High Ambiguity Driven protein-protein DOCKing, at Univ. Utrecht
SmoothDock - Docking, pure and simple, at Univ. of Pittsburgh
FireDock - Refinement and re-scoring of protein-protein docking solutions, at Tel-Aviv University
SymmDock - predicts symmetrical complexes of a single molecule, at Tel Aviv Univ.
PatchDock - docking based on shape complementarity, at Tel Aviv Univ.
HEX - fairly straightforward docking, at Univ. of Aberdeen (doesn't work with firefox)
RosettaDock - short-range local docking search using Rosetta, at Johns Hopkins Univ.
DBD_Hunter - predicts DNA-binding protein function, at Georgia Tech Univ.
ZDOCK - fast-fourier based protein docking, very fast, at Boston Univ.
GRAMM-X - rigid body, FFT-based protein docking, at Kansas Univ.

Protein Structure Refinement and Analysis

CaspR - automated molecular replacement server, CNRS
TB Consortium - electron density map improvement server, Texas AM University
PoseViewWeb - automatic 2D ligand complex diagrams, at Universität Hamburg
molmovdb.org - Database of Macromolecular Movements with Associated Tools, at Yale
HingeProt - Protein hinge prediction using elastic network models
IntAct - database system and analysis tools for protein interaction data, at EBI
Fold Space Navigator - Quantitative classification, efficient navigation, and instantaneous visualization of similarities, at University of Salzberg
ModFOLD - Assessment of protein structure quality, at University of Reading
NQ-Flipper - Flip those asparagines and glutamines!
ERIS - Protein stability prediction server, at UNC
MOLEOnline - Find and analyze molecuar channels, tunnels, and pores, at Univ. Palackeho
PROPKA2.0 - Fast calculation of protein PKas, at Univ. of Copenhagen
MolAxis - Accurate Identification of Channels in Macromolecules, at Tel Aviv Univ.
ConSurf - Predicts functional regions in proteins based on phylogeny, at Tel Aviv Univ.
HELIQUEST - Analyse alpha-helical sequence and identify protein segments from a database, at CNRS
AUTO-MUTE - Automated server for predicting functional consequences of amino acid mutations, at George Mason Univ.
MSX-3D - Determine distance constraints from cross-linking and mass spectrometry, at PBIL, Lyon, France

Protein Structure Alignment

TOPOFIT-DB - Database of structural alignments based on the TOPOFIT method
HOMSTRAD - Homologous Structure Alignment Database, at University of Cambridge
Protein Blocks Expert - Structural alignment using structural alphabets, at Université de La Réunion
Cathedral - Find the closest protein fold group for a given structure, at CATH
PRIDE2 - Calculate probability of identity between structures, at ICGEB
TopMatch - cool web-based structural alignment tool, requires IE and Jmol, at University of Salzberg
Vorometric - structurally search for alignments, at Ohio State Univ.