Sequences

Structure

Protein Structure Modeling

Small Compounds

Sequences

Search

Analysis

Alignement

Convert

Structure

Search

Edit

Superpose 2 structures

Analyse

Protein Structure Modeling

model banks

Structural prediction

Automated model building

Evaluation of model quality

Small Compounds

FAFDrugs

Pockets

Screening Test Sets

Utilities

Sequences Search   from a keyword > return      PubMed  external ressource          search pubmed

SRS  external ressource          Sequence Retrival System

SwissProt  external ressource          search swissprot

from a sequence      AutomatP  available in p-server          Search for homologous sequences and align them with your query

AutomatN  available in p-server          Search for homologous sequences and align them with your query (nucleic acids)

psiBlast  RPBS services - available in p-server          run psi-blast on your sequence

Prosite  external ressource          Scan prosite

ProDom  external ressource          Scan ProDom

PDB      PDBSeqres  available in p-server          PDB Sequences

Analysis   Composition > return      MM-PI-Composition  external ressource          Some properties such as Molecular Weigth, pI, ...

Motifs      MotifScan  external ressource          Search your sequence for known motifs

InterProScan  external ressource          Search your sequence for known motifs

Hydrophobicity      HCA  available in p-server          Draw an HCAplot - Based on Hydrophobic Cluster Analysis

Function      ProtFun  external ressource          Predict function from protein sequence

Useful links      Infobiogen  external ressource          Infobiogen Sequence analysis tools

Expasy  external ressource          ExPASy Catalogue of Proteomics tools

Alignement   Sequence alignement > return      clustalw  RPBS services - available in p-server          Multiple sequence alignement, limited to protein sequences

tcoffee  RPBS services - available in p-server          Multiple sequence alignement

Convert   Sequence Format conversion > return      squizz  RPBS services - available in p-server          Format conversion of sequence files.

Structure Search   search the PDB > return      PDBlite  external ressource          Interface to PDBlite service.

MSDlite  RPBS services - available in p-server          Simple search of relational PDB

from a sequence      Blast  RPBS services - available in p-server          Search for sequence from PDB entry similar to that of your query using Blast.

SAM-t02  external ressource          HMM-based threader Protein Structure Prediction

3DPSSM  external ressource          3D-PSSM profile threader Protein Structure Prediction

123D  external ressource          123D threader

Browse classifications of protein structures      SCOP  external ressource          SCOP: Structural Classification of Proteins

CATH  external ressource          CATH: automated Protein Structure Classification

SARF-tree  external ressource          SARF: classification of structures

ASTRAL  external ressource          ASTRAL

from a structure      Yakusa  available in p-server          Recherche rapide dans une base de structure protéique PDB

SA-search  available in p-server          Search for similar 3D structures (based on structural alphabet)

CE-all  external ressource          Search the PDB for a structures similar to yours using CE

DALI-all  external ressource          Search the PDB for a structures similar to yours using DALI

VAST  external ressource          Search the PDB for a structures similar to yours using VAST

MATRAS-all  external ressource          Search the PDB for a structures similar to yours using MATRAS

Utilities      PDBTM  RPBS services - available in p-server          3D transformation

PDBPileUp  external ressource          multiPDB file generation

PDBpart  external ressource          PDB part extraction

Edit   Dihedrals > return      BasicBuilder  available in p-server

Substitutions  available in p-server          Sub service of SCit, a set of tools for protein side chain conformation analysis and editing

HydrogenBuilder  available in p-server          Hydrogen positionning

Superpose 2 structures   User provided alignment > return      Superpose  available in p-server

Automated search      CE  external ressource          Pairwise comparison of 2 strcutures using CE

DALI  external ressource          Pairwise comparison of 2 strcutures using DALI

K2  external ressource          Pairwise comparison of 2 strcutures using K2

SARF  external ressource          SARF structural alignement

MATRAS  external ressource          MATRAS structural alignement of 2 structures

Analyse   Dihedrals > return      phi-psi  available in p-server          protein backbone

SCit  available in p-server          Side chain conformation analysis and editing

Secondary structure      stride  RPBS services - available in p-server          Identify secondary structures

p-sea  RPBS services - available in p-server          Identify secondary structures

extract-Turn  available in p-server          Beta turn identification

HMMSA-Encoder  available in p-server          Structure encoding as letters of a structural alphabet Hidden Markov Model derived

Hydrogen bonds      H-bonds  available in p-server

Solvent accessible surface area      ASA  available in p-server

VADAR  external ressource          VADAR (Volume, Area, Dihedral Angle Reporter) suite of services

Electrostatics      mead-pKa  available in p-server          Calculate a protein pKa

mead-pot  available in p-server          Calculate the electrostatic potential and display a graphic view of results

Domains      3Dee  external ressource

PDP  external ressource

Protein Structure Modeling model banks   model banks > return      ModBase  external ressource          Database of hree-dimensional comparative protein structure models, at Sali lab.

SwissModel  external ressource          Database of three-dimensional comparative protein structure models, maintained at expasy.

Structural prediction   Secondary structure > return      psi-Pred  RPBS services - available in p-server          method for protein secondary structure prediction

Jnet  RPBS services - available in p-server          Jnet - Method of protein secondary structure prediction

PROF  external ressource          PROF - Secondary Structure Prediction System at Aberystwyth, Wales

COUDES  external ressource          Beta turn prediction from sequence

Local Structure      LocPred  external ressource          Prediction of protein local conformation, using protein blocks structural alphabet

Acessible surface Area      PredAcc  available in p-server          Prediction of solvent accessibility

NetASA  RPBS services - available in p-server          Prediction of solvent accessibility using a neural network algorithm

RVP-net  external ressource

Disulfide bridges      CysState  available in p-server          Cysteine oxydation state from sequence

Cystein bonding and connnectivity  external ressource          Prediction of disulfide bonding state and connectivity pattern of the cysteines given a sequence

Automated model building   Homology modeling > return      CBSmetaserver  external ressource          Homology modelling server

Geno3D  external ressource          Homology modelling server

Ab initio modeling      HMMStr  external ressource          HMMStr server (Rosetta)

Evaluation of model quality   Structure validation services > return      Eval123D  external ressource          Structure validation suite service at CBS (Montpellier, France)

PROCHECK  external ressource

verify3D  external ressource          VAnalysis of the quality of a putative crystal structure for protein

Biotech validation suite  external ressource

Aqua  external ressource

Small Compounds FAFDrugs   ADME-Tox filter > return      ADMETox  available in p-server          adme-tox filter.

Collections of small compounds      Collections  available in p-server          Collections of small compounds

AmbInter  available in p-server          Ambinter 2008

Pockets   Pocket identification > return      PASS  RPBS services - available in p-server          Putative Pocket identification from Protein Structure.

Screening Test Sets   In silico Screening > return      TestSets  available in p-server          Test sets for in silico screening.

Utilities   octanol-water partition > return      LogP  RPBS services - available in p-server          logP calculation

Salt removal      DeSalt  RPBS services - available in p-server          Salt removal

Format conversion      OpenBabel  RPBS services - available in p-server          Data format conversion

Graphical Editor      JME  RPBS services - available in p-server          Molecular Editor