Sequence Searches and Analysis

• BLAST and PHI-BLAST at NCBI
• BLASTPAT  Search of a Pattern Database with a Query Protein Sequence
• BEAUTY  Protein Sequence Searches using the BCM Launcher
• PepPepSearch Search SwissProt for a peptide sequence
• ProfileScan  Server Search a protein sequence against a profile database
• PeptideSearch Protein identification by peptide mapping or peptide sequencing
• Blocks WWW Server Query sequence comparison against the BLOCKS database of highly Conserved Regions of Protein
• SW-SSEARCH Sequence searches using the Smith-Waterman Algorithm
• Scanps2.3 (New Version) Fast implementation of the Smith & Waterman algorithm for protein database searches

Protein Motif Searches

• PatternFind Search a protein sequence database with a pattern.
• PrositeScan Search PROSITE with a sequence. This is a PERL-implementation of a program searching the current release of the PROSITE database using regular expressions.
• PATTINPROT Scans a protein sequence or a protein database for one or several pattern/s.
• FingerPRINTScan PRINTS Protein fingerprint searches.
• PPSEARCH Protein Motif Search at EBI
• PRATT Protein Motif Discovery

Primary Structure Analyses

• SAPS Statistical Analysis of Protein Sequences. This program analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output.
• 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
• COILS Prediction of Coiled Coil Regions in Proteins. The program predicts (2 stranded) coiled coil regions in proteins by the Lupas-algorithm.
• PEST Sequence Searches. PEST regions are present in proteins with short half-lives. 

Secondary Structure Prediction

• PREDATOR  Secondary Structure Prediction from single or multiple sequences; no web interface at present
• PredictProtein  predicts different aspects of protein structure.
• The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
• HNN - Hierarchical Neural Network method for secondary structure prediction
• PSIRED predict structural information on proteins using several methods (PSIRED, GenTHREADER, MEMSAT2)
• SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology)
• TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
• TMpred Prediction of Transmembrane Regions and Orientation. The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins.
• TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)

Post-translational Modification Predictions

• PSORT - Prediction of protein sorting signals and localization sites
• SignalP - Prediction of signal peptide cleavage sites
• ChloroP - Prediction of chloroplast transit peptides
• MITOPROT - Prediction of mitochondrial targeting sequences
• NetOGlyc - Prediction of type O-glycosylation sites in mammalian proteins

Protein Databases & Retrieval

• InterPro provides an integrated view of the commonly used protein signature databases, and has an intuitive interface for text- and sequence-based searches.
• DBGET Integrated Database Sequence Retrieval Server (keyword searches).
• SWISS-PROT is a curated protein sequence database which provides a high level of annotations.
• TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT
• DIP (Database of Interacting Proteins) is a database of protein pairs that are known to interact with each other.
• POWL Keyword Search of PIR Database
• GCR-DB G-Coupled Protein Receptor Database
• Entrez Protein Retrieval at NCBI
• TRANSFAC provides information on transcription factors, their binding sites and binding profiles. Also available are sequence analysis tools for potential transcription factor binding sites. 

Protein Identification based on physical & chemical data

a) Protein Identification based on pI,  Molecular Mass, Peptides

• MultiIdent  Experimental pI & Mass Data comparison against SwissProt sequences. 
• TagIdent Tool - pI & Mr-based Search of SwissProt database at ExPasy
• PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data.
• CombSearch An experimental unified interface to query several protein identification tools accessible on the web
• MOWSE (MOlecular Weight SEarch) searches the owl protein sequence database with protein fragment information.
• Mascot Peptide mass fingerprint, sequence query and MS/MS ion search from Matrix Science, London
• ProFound Protein identification by comparison of a peptide map to NCBI's non-redundant database.
• PeptideSearch Protein identification by peptide mass data. (Edman degradation)
• PepFrag Protein Identification by Comparison of the Fragmentation Pattern of a Peptide to a Database
• MS-Fit A peptide mass fingerprinting tool that tries to fit a user's mass spectrometry data to a protein sequence in an existing database.

b) Protein Identification based on Amino Acid Composition

• PropSearch uses the amino acid composition, properties like molecular weight, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. to identify proteins.
• AACompIdent  identifies a protein by its amino acid composition
• AACompSim  compares the amino acid composition of a SWISS-PROT entry with all other entries

c) general

• Protein Prospector The site has a range of tools for mining sequence databases in conjunction with Mass Spectrometry and Proteomic experiments.
• 3D-PSSM - The 3D-PSSM server is a designed to take a PROTEIN sequence of interest and attempt to predict its 3-dimensional structure and its probable function.

2 D-PAGE Databases & Information

a) Databases

• Plant Plasma Membrane Database (Arabidopsis) at Gent University (the DB is no longer updated)
• Maize 2D Protein Database at INRA
• 2-D gels for maritime pine at INRA, Bordeaux, France
• NCI 2DWG Image Meta-Database Catalog of 2D PAGE gel images found in Web databases.
• NCI's Partial List of Web 2D Electrophoretic Gel Databases.
• SWISS-2D PAGE contains data on proteins identified on various 2-D PAGE reference maps.
• Several 2D PAGE databases are located at the Danish Centre for Human Genome Research. Also available are 2D Gel Galleries of Human and "Zoo Species".

b) Technical Info and Link Pages

• 2-D PAGE technical Information developed by the Electrophoresis Laboratory at Geneva University Hospital offers a range of protocols.
• The 2D Gel Electrophoresis Tutorial at Aberystwyth, UK.
• Tutorial on Two-Dimensional Electrophoresis of Proteins using Immobilized pH Gradients at the TU Munich, Germany.
• Technical Information for in-gel digestion procedure used at the UCSF Mass Spectrometry Facility for generating and recovering peptides from proteins isolated by gel electrophoresis in a manner compatible with subsequent delivery to a MALDI-TOF mass spectrometer
• 2D Hunt "2-D electrophoresis Finder" (search engine) 
• Melanie The 2D Gel Analysis Software. 
• FLICKER  Web Server for Comparing images across the Internet
• CAROL - 2D Gel Matching program
• WORLD-2DPAGE Index to 2D PAGE databases and services
• Guidelines for building a federated 2-DE database 

Protein Modelling

• 3Dee Database of Protein Domain Definitions
• SWISS-MODEL is an automated knowledge-based protein modelling server
• CPHmodels - predicts protein structure using comparative (homology) modelling (automated neural-network based protein modelling server)
• Raster3D Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
• MODBase  is a queryable database of annotated protein structure models. The models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER.
• Biotech Validation Suite for Protein Structures
• The NRL_3D Sequence-Structure Database is produced by PIR from sequence and annotation information extracted from three-dimensional structures in the Protein Databank (PDB).
• Sting Millennium Suite - Protein Dossier This service provides a graphical report of several important structural characteristics of the PDB entry.

Model Viewing Tools

• Swiss-PdbViewer A program to display, analyse and superimpose protein 3D structures
• RasMol RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
• Cn3D - Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
• Hyperactive Molecules Using Chemical MIME - WWW Display of 3D Chemical Information - Imperial College (UK)
• MOLMOL  is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.
• VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code.
• A List of Molecular Graphics Applications used in macromolecular structure determination, analysis and display can be found at Yale University.

Crystallography

• Software and Tutorial for Crystallography
• Protein Crystallography  at Glasgow Uni, UK
• Crystallization Techniques at the Scripps Institute
• NeXus Software Library's Crystallographic software