Archive for the Structural Bioinformatics Category

Structural Bioinformatics

Posted on décembre 6, 2009 by Commentaires fermés sur Structural Bioinformatics

A large number of tools are provided by ReNaBi’s platforms.

Docking@Grid Conformational Sampling and Docking on Grids
FROST Fold recognition (threading) program
OSS-HMM Protein secondary structure prediction program
KAKSI Protein secondary structure assignment program
VAST 3D structure comparison program
NPS@ Web tools for protein structure analysis
Geno3D Automatic modelling of protein 3D structure
SOPMA Prediction of secondary structure of proteins
MLRC Prediction of secondary structure of proteins
DPM Prediction of secondary structure of proteins
SUMO Sites detection in proteins
ESPript/ENDscript Extracting and rendering sequence and 3D information from atomic structures of proteins
SOPM Prediction of secondary structure of proteins
HCA Hydrophobic Cluster Analysis

Many other tools are available. Here is a listing classified according to 4 categories :

Tertiary Structure

  • 3D structures superimposition (NPS@) available at the PRABI
  • ATOME available at Montpellier: @utomatic Threading Optimisation Modelling & Evaluation
  • CaspR available at Marseille: An automated approach for molecular replacement
  • COSA Pasteur Paris Clustal ouput structural analysis
  • COUDES online RPBS web server for beta-turn prediction
  • ElNémo: Marseille The Web-interface to The Elastic Network Model, a fast and simple tool to compute the low frequency normal modes of a protein
  • ESAP: MIG Jouy Prediction of protein loop conformation
  • Geno3D : PRABI Automatic molecular modeling
  • IMGT/StructuralQuery: Montpellier Retrieval of IMGT/3Dstructure-DB entries using domain type and/or position structural criteria
  • KinDOCK server : Montpellier Ligand Transposition Server
  • LocPred online: RPBS Local structure prediction
  • PAT server: PAT (Protein Analysis Toolkit) Montpellier toolkit to facilitate the combination of different processing tools for more complex protein analyses
  • PPG online: RPBS Protein Picture Generator
  • SA-Search online : RPBS search for 3D fragments similar to (fragments of) a query structure
  • SCit online: SCit RPBS Tools for protein side chain conformation analysis and editing
  • Small compounds: RPBS project involving the screening of databases of small chemical compounds
  • SuMo : Surfing the Molecules – Search for similar 3D sites in proteins
  • WLoop online: RPBS predict protein loop backbone structures from their sequences and their flank backbone structures
  • XmMol: RPBS desktop macromolecular visualization and modeling tool

Secondary Structure

  • Dicroprot: a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments
  • Gor IV: (MIG) method for predicting protein secondary structure from amino acid sequence
  • HCA online: Hydrophobic cluster analysis
  • PAT server: toolkit to facilitate the combination of different processing tools for more complex protein analyses
  • sspred toolkit: Secondary structure prediction
  • Simpa: MIG Jouy protein secundary structure prediction based on the « nearest-neighbor » notion

Cristallography

  • SAmBA online: Marseille, Interactively computes the experimental protocol corresponding to your combination of variables and states

NMR Tools

  • CINDY: Graphical NMR assignment software
  • CROWD:
  • GIFA: NMR processing program which includes many signal processing methods, such as Maximum Entropy, Linear Prediction, automatic Phasing, line fiting, base line correction…
  • RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins

Filed Under: Structural Bioinformatics