WEB SITES USED IN THE COURSE

Protein structure retrieval and visualization

The Protein Data Bank
MolMol home page
PyMOL

Data Banks, sequence search, and alignment

NCBI - National Center for Biotechnology Information (NCBI) home page
BLAST (Basic Local Alignment Search Tool): Sequence similarity search at NCBI
    Basic BLAST search
    Advanced BLAST
    Psi-BLAST: Position-Specific Iterated BLAST: a sensitive way to look for homologues
    Phi-Blast to search for motifs

The EMBL-European Bioinformatics Institute (EBI), UK
Database searching using the Sequence Retrieval System, version 6.0 (SRS6)

SWISS-PROT and TrEMBL at ExPASy (Expert Protein Analysis System)
SWISS-PROT full text search using SRS6
ClustalW Multiple Sequence Alignment

Protein Sequence Alignment and Database Scanning:
Geoffrey J. Barton in Protein Structure Prediction -  A Practical Approach, Edited by MJE Sternberg (Oxford University Press)

Secondary structure prediction

A. General

Guide to prediction and Flow-chart
Secondary Structure Prediction: Different Methods

B. Methods using single sequences

The most comprehensive web server for secondary structure prediction is Jpred2:
Introduction/information    Jpred3:Submit your sequence
 
The Chou & Fasman Prediction:  One of the earliest sec. str. prediction methods

   Chou-Fasman input form
 
Network Protein Sequence Analysis: Home page
Geourjon & Deleage, IBCP, France

GOR(Garnier, Osguthorpe, Robson):context dependent propensity for secondary structure
    Input form for GOR method
nnPredict: A neural network method (Cohen et al., UCSF)

    nnPredict: Input Form

BMERC PSA (Protein Sequence Analysis)

Probabilistic discrete state space method (smoothing and filtering functions)
     BMERC PSA: input form

 C. Methods using multiple sequence alignments

DSC: Discrimination of Protein Secondary Structure Class (King & Sternberg)
The method is based on the GOR approach and mean moment of hydrophobicity.

Linear discrimination method is used for the final prediction. Original DSC currently
unavailable; Program 'Prof' or 'Son of DSC' can be accessed at the following link:
    Prof: Input form
 
PREDATOR: Frischman & Argos (EMBL): Info page
Propensity of secondary stgructure, hydrogen bonded residues, pair-wise alignment
 
The PredictProtein Home Page: Rost, B: Columbia University

"You submit any protein sequence. PredictProtein retrieves similar sequences in the database
 and predicts aspects of protein structure"
   The PredictProtein: input form
 
PCPMer: Home page
"PCPMer is a software package for determining conserved regions in multiple sequence alignments.", developed in W.Braun's group


Search for Other Structural Features

COILS: to predict coiled-coil structures
PROSITE database of protein families and domains

Domain identification

Pfam: Protein families database of alignments and HMMs
Search Pfam
Material on Hidden Markov Models (UC Santa Cruz)

The ProDom protein domain database: Home page and starting point for searches
A compilation of homologous domains, searcheable in different ways

ICGEB: International Centre for Genetic Engineering & Biotechnology, Trieste, Italy
    The SBASE 7.0 Protein domain library and search tools

Protein Fold Recognition/ Threading

SCOP: Structural Classification of Proteins
 "structural and evolutionay relationships between all proteins whose structure is known".
Can be accessed in four of different ways starting from the above link.

TOME 

FUGUE  Sequence-structure homology recognition

3D-PSSM web server, Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London
"A fast web-based method for Protein Fold Recognition using 1D and 3D Sequence
Profiles coupled with Secondary Structure and Solvation Potential Information"

      phyre "Protein Homology/analogY Recognition Engine".  You are advised to use the NEW Phyre fold recognition system. It is more accurate and more up to date than 3D-PSSM.


GenThreader, from PSIpred, Protein Bioinformatics Group, Department of Biological Sciences, University of Warwick
     PSIpred Input form
 
TOPITS, PredictProtein server @ Columbia University

Threading a sequence through a set of structures: 123D+ Homepage
    123D+ input form

FFAS

Karplus 1 & 2

Karplus 3

      SAM-T02 "HMM-based Protein Structure Prediction"

Homology Modeling (Comparative Modeling)

Swiss-Model Home page
WHAT IF interface at EMBL, Heidelberg

Ab initio Protein Modeling

CASP: Protein structure prediction center
PCPMer: Home page

Protein Structure Analysis and Validation

PROCHECK Home page: How to download, install, and run the program

To check the stereochemical quality of a protein structure
 
WHAT IF: Home page

A general protein structure analysis program.
WHAT_CHECK: protein structure verification tools from WHAT IF 

 
SCSBMB Software Links

PCPMer:        A set of Physical Chemical Property based Motif Analyzer tools.

InterProSurf:  Tool for prediction of functional sites in protein monomer surfaces.

GETAREA:   Program developed in our group to calculate Solvent Accessible Surface Areas, Atomic Solvation Energies,
and their Gradients for macromolecules.