Structural Analysis
The Dali server is a network service for comparing protein structures in 3D. Access also to related tools: SRS search for FSSP (families of structurally similar proteins); search for DSSP; search for HSSP, (homology-derived structures of proteins), a derived database merging structural (2-D and 3-D) and sequence information (1-D).
http://ekhidna.biocenter.helsinki.fi/dali_server/
PDBeMotif is an extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search. Currently it is the only tool that offers this kind of integration at this speed. PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins such as Kinases and the conserved structural features of their immediate environments either within the same specie or across different species.
http://www.ebi.ac.uk/pdbe-site/pdbemotif/
The WHAT IF Web Interface proposes a varied set of analyses on protein structure.
http://swift.cmbi.ru.nl/servers/html/index.html
The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods (see below) to try to provide clues as the the protein's likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful.
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions;
http://crick.mbu.iisc.ernet.in/~PIC/
PRIDE2 server calculates the PRobability of IDEntity between three-dimensional domains (or whole structures) and offer varied various compararisons with known structures (from fold identification, CATH and PDB search, to NMR-NOE set comparison).
http://hydra.icgeb.trieste.it/pride/index.html
PBE server 2.0 aims to provide a platform for protein structure
http://bioinformatics.univ-reunion.fr/?page_id=153
The ConSurf server is a useful and user-friendly tool that enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure, based on the phylogenetic relations between its close sequence homologues.
http://consurf.tau.ac.il/
StrucToolsn is a set of tools intended to provide a convenient web interface to simple, commonly used structural biology calculations with PDB files.
http://helixweb.nih.gov/structbio/basic.html
STING Millennium is a web based suite of programs that starts with the visualization of a molecular structure and leads the user through a series of operations resulting in an extensive structural analysis of the molecule
http://luna.bioc.columbia.edu/SMS/sms.html
firestar server: predicting functional residues from structural templates and alignment reliability
http://firedb.bioinfo.cnio.es/Php/FireStar.php
Evaluating the salt brIdges in proteins.
http://bioinformatica.isa.cnr.it/ESBRI/introduction.html
This program allows to analyse contacts between two chains or within one chain in a given PDB file.
http://ligin.weizmann.ac.il/cma/
HORI - Higher Order Residue Interactions, is a web server to compute higher order interactions (pairwise interaction, triplet interactions and quadruple interactions) in a protein structure.
http://caps.ncbs.res.in/hori/
MolTalk is a computational environment for doing Structural Bioinformatics. At the base of i.Moltalk
http://www.moltalk.org/
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
http://foldx.crg.es/
Web resource for the identification of sequence-structure links. The resource consists of an exhaustive collection of annotated links between the Swiss-Prot + TrEMBL sequence database entries and the PDB and SCOP structure database entries.
http://surface.bio.uniroma2.it/seq2struct/
iMolTalk is an interactive, Internet-based service for computational analyses in Structural Biology that Compute Ramachandran plot (?/? angles), Compute Distance Matrix of C? atoms, Find Contacts for a residue or Distances between a pair of residues, Find Interface between two chains of a structure, Compute Secondary structure assignment, Structural Alignment Structural Alignment computation, derivation and verification. Structurally compare all models in a structure, and Analyse Domain Motion Analyse domain motion in homologous structures.
http://i.moltalk.org/
MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimised in rotamer space using a rough potential energy function to avoid clashes.
http://www.ebi.ac.uk/maxsprout/
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