Bioinformatics Links Directory : Biochemical Features

The resources in this section include protein identification tools as well as tools which can give you information on the chemical structures and amino acid properties of peptide sequences.

WebProAnalyst - (Found June 19, 2008 )

WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.
http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/

ProMoST - (Found June 19, 2008 )

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.
http://prometheus.brc.mcw.edu/promost/

PROFEAT - (Found June 19, 2008 )

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence.
http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

pKD - (Found June 19, 2008 )

pKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change.
http://polymerase.ucd.ie/cgi-bin/pKa_Design/server_start.cgi

PI2PE - (Found June 19, 2008 )

PI2PE (Protein InterfaceInterior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.
http://pipe.scs.fsu.edu/

PHEPS - (Found June 19, 2008 )

pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.
http://pheps.orgchm.bas.bg/home.html

PeptideMass - (Found June 19, 2008 )

Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.
http://us.expasy.org/tools/peptide-mass.html

PDB_Hydro - (Found June 19, 2008 )

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.
http://lorentz.immstr.pasteur.fr/solvate_mutate.php

PDB2PQR Server - (Found June 19, 2008 )

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.
http://pdb2pqr.sourceforge.net/

ProSight PTM - (Found June 19, 2008 )

ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the 'Top-Down' tandem mass spectrometry (MSMS) approach.
http://prosightptm2.scs.uiuc.edu/