Protein Analysis

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
Submitted: Sep 11, 2000
PASS (Putative Active Sites with Spheres) is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes.
Submitted: Dec 10, 2000
A program for spatial arrangement of backbone fragments in protein structures.
Submitted: Sep 06, 2000
Atlas of Protein Side-Chain Interactions  
This atlas depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.
Submitted: Oct 19, 2000
Tools for mining sequence databases in conjunction with Mass Proteometry experiments.
Submitted: Oct 19, 2000
CLUSPROT is a program that delineates spatial clusters in protein structures on the basis of atomic contacts between residues. The program allows for clustering of side-chains, main-chains, main-chains and side-chains, etc. The program reads files with protein structures that are in Brookhaven Protein Data Bank format.
Submitted: Oct 19, 2000
TALOS is a database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence. The TALOS approach is an extension of the well-known observation that many kinds of secondary chemical shifts (i.e. differences between chemical shifts and their corresponding random coil values) are highly correlated with aspects of protein secondary structure. The goal of TALOS is to use secondary shift and sequence information in order to make quantitative predictions for the protein backbone angles phi and psi, and to provide a measure of the uncertainties in these predictions.
Submitted: Oct 15, 2000
WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
Submitted: Sep 15, 2000
The program takes the protein sequences of one or two databases and creates protein families. The protein sequence databases can be a whole genome, part of a genome or any other protein sequence databases in fasta format.
Submitted: Sep 07, 2000
LIBRA is the name of a computer application for analyzing protein structures and sequences. The basic methodology used is "Threading", which means that LIBRA evaluates the compatibility of a protein structure and a sequence.
Submitted: Sep 16, 2000
Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
Submitted: Sep 06, 2000
Knowledge - based protein secondary structure assignment from atomic coordinates. Performs the same task as DSSP by Kabsch and Sander but utilizes both hydrogen bond energy and mainchain dihedral angles rather than hydrogen bonds alone.
Submitted: Oct 19, 2000  
Specializing in microarray analysis, bioinformatics, and expression gene profiling service.
Submitted: Dec 10, 2003
MultiIdent Tool  
MultiIdent is a tool that allows the identification of proteins using pI, MW, amino acid composition, sequence tag and peptide mass fingerprinting data. One or more species and a SWISS-PROT keyword can also be specified for the search.
Submitted: Oct 19, 2000
To maximize the chances of biological discovery, homology searching must use an up-to-date combination of multiple sequence databases. nrdb90 clusters the sequence database yielding a representative subset that is faster to search and improves the consistency of sequence annotation. The generation of a representative set is effectively an all-against-all comparison problem. nrdb90 uses a fast and complete lookup algorithm for the removal of fragments and close similarities. Search space is pruned using deca- and pentapeptide composition filters that leave a minimal fraction of pairs for which sequence identity is determined by explicit alignment.
Submitted: Oct 07, 2000
3DCrunch is a Very Large Scale Protein Modelling Project, which was run from May 18 to 20 at the Silicon Graphics Advanced Technology Center in Cortaillod (Ne) Switzerland.
Submitted: Oct 19, 2000
AACompIdent Tool  
AACompIdent is a tool which allows the identification of a protein from its amino acid composition [references]. It searches the SWISS-PROT and / or TrEMBL databases for proteins, whose amino acid compositions are closest to the amino acid composition given.
Submitted: Oct 19, 2000
FindMod is a tool that can predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides.
Submitted: Oct 22, 2000
The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine.
Submitted: Oct 19, 2000
PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in the SWISS-PROT/TrEMBL databases. A species (or group of species) can also be specified for the search.
Submitted: Oct 19, 2000
The Pratt program is able to discover patterns conserved in sets of unaligned protein sequences. On these pages you will find information about Pratt, related publications, and PrattWWW: a WWW interface that allows you to use Pratt on-line.
Submitted: Sep 09, 2000
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Submitted: Sep 15, 2000
TagIdent is a tool which allows the generation of a list of proteins close to a given pI and Mw, the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the SWISS-PROT/TrEMBL databases close to a given pI and Mw, the identification of proteins by their mass, if this mass has been determined by mass spectrometric techniques.
Submitted: Oct 19, 2000

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