Structural Bioinformatics
Posted on décembre 6, 2009 by adminCommentaires 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