Alexandre G. de Brevern's Tools

Please find here links to some of my developments.

Protein Superimposition

Faure G., Joseph A.P., Craveur P., Narwani T.J., Srinivasan N., Leonard S., Gelly J.-C., Rebehmed J., de Brevern A.G.^#
iPBAvizu: a PyMOL plugin for an efficient 3D protein structures su-perimposition approach
to be submitted .
iPBAvizu (iPBA plug-in for PyMOL software).
Leonard S.^*, Joseph A.P.^*, Srinivasan N., Gelly J.-C., de Brevern A.G.^#
mulPBA : an efficient multiple protein structure alignment method based on a structural alphabet
J Biol Struct Dyn (2014) 32(4):661-8.
mulPBA (multiple protein 3D structure superimposition).
Mahajan, S., Iftekar M., Agarwal G., Offmann B., de Brevern A.G., N. Srinivasan^#
DoSA: Database of Structural Alignments
Database (2013) 2013:48.

DoSA The Database of Structural Alignments (DoSA) realigned structurally variable regions (SVRs) using an algorithm based on protein blocks.
J.-C. Gelly, Joseph A.P., Srinivasan N., de Brevern A.G.^#
iPBA : A tool for protein structure comparison using sequence alignment strategies
Nucleic Acid Res (2011) 39:W18-23..
iPBA (pairwise protein 3D structure superimposition and PDB mining).
Mahajan, S., Iftekar M., Agarwal G., Offmann B., de Brevern A.G., N. Srinivasan^#
DoSA: Database of Structural Alignments
Database (2013) 2013:48.
DoSA (database of protein 3D structure superimposition re-alignment).
Tyagi M., Sharma P., Swamy C.S., Cadet F., Srinivasan N.^#, de Brevern A.G., Offmann B.
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet
Nucleic Acids Res. (2006) 34(Web Server issue) W119-23.
see now iPBA.

Protein Peeling

Gelly J.-C.^#, de Brevern A.G.
Protein Peeling 3D: New tools for analyzing protein structures.
Bioinformatics (2011) 27(1):132-3.
PP3 Determination of Protein Units and Protein Structural Domains.
Gelly J.C., Etchebest C., Hazout S., de Brevern A.G^#
Protein Peeling 2: a web server to convert protein structures into series of protein units
Nucleic Acids Res. (2006) 34(Web Server issue) W75-8
see now PP3.
Gelly J.C., de Brevern A.G^#, Hazout S.
Protein Peeling: an approach for splitting a 3D protein structure into compact fragments
Bioinformatics (2006) 22(2) 129-33
see now PP3.

Protein Structure analysis

Barnoud J., Santuz H., Craveur P., Joseph A.P., Jallu V., de Brevern A.G., Poulain P.^#
PBxplore: A Tool To Analyze Local Protein Structure And Deformability With Protein Blocks
submitted
PBxplore PBxplore is a suite of tools dedicated to the analysis of Molecular Dynamics simulations with Protein Block (PB) structural alphabet.
Chebrek R., Leonard S., de Brevern A.G., Gelly J.-C.^#
PolyprOnline : Polyproline helix II and secondary structure assignment database
Database (2014) pii: bau102.

PolyprOnline PolyprOnline is A database dedicaced to Polyproline II Helix conformations in proteins.
Craveur P.^*,#, Rebehmed J.^*, de Brevern A.G.^#
PTM-SD: a database of structurally resolved and annotated post-translational modifications in proteins
Database (2014) 2014: bau041.

PTM-SD Posttranslational modification structural database (PTM-SD) provides access to structurally solved modified residues, which are experimentally annotated as PTMs.
Esque J.^*, Leonard S.^*, de Brevern A.G.^+,#, Oguey C.^+,#
VLDP webserver: a powerful geometric tool for analysing protein structures in their environment
Nucl Acid Res (2013) 41:W373â€“378.
VLDP Amino acid volumes, accessibility and contact determination.
Martin J.^#, Letellier G., Marin A., Taly J.-F., de Brevern A.G., Gibrat J.-F.
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods
BMC Structural Biology (2005) 5:17.
KAKSI secondary structure assignment [local website: KAKSI].

Protein prediction

Vetrivel V., Mahajan S., Tyagi M., Hoffmann L., Sanejouand Y.-H., srinivasan N., de Brevern A.G., Cadet F., Offmann B.^#
PB-kPRED: Knowledge-Based Prediction Of Protein Backbone Conformation Using A Structural Alphabet
submitted
PB-kPRED FoRSA provides a unique fold recognition algorithm which is based on calculation of conditional probability for the amino acid sequence of a protein to fit to a particular fold.
Ghouzam Y., Postic G., Guerin P.E., de Brevern A.G., Gelly J.-C.^#
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.
Sci Rep (2016) 6:28268.
ORION ORION (Optimized protein fold RecognitION) is a sensivitve method for protein template detection. ORION is based on a profile-profile approach that relies on a better description of the local protein structure to boost distantly protein detection.
Mahajan S., de Brevern A.G., Sanejouand Y.-H., Srinivasan N., Offmann B.^#
Use of a structural alphabet to find compatible folds for amino acid sequences
Protein Science (2015) 24(1) 145Â–153.
ForSA FoRSA provides a unique fold recognition algorithm which is based on calculation of conditional probability for the amino acid sequence of a protein to fit to a particular fold.
Etchebest C.^*, Craveur P.^*., Narwani T.J.^*., Bornot A., Leonard S., Poulain P., Rebehmed J., Gelly J.-C., de Brevern A.G.
in silico protein prediction flexibility with local protein structure approach
to be submitted .
PredyFlexy 1.3 Software tools to do protein structure flexibility prediction from the sequence.
de Brevern A.G.^#, Bornot A.*, Craveur P., Etchebest C., Gelly J.-C.
PredyFlexy: Flexibility and Local Structure prediction from sequence
Nucleic Acid Res (2012) 40:W317-22.
PredyFlexy Prediction of protein structure flexibility from the sequence.
de Brevern A.G.^#, Benros C., Gautier R., Valadié H., Hazout S., Etchebest C.
Local backbone structure prediction of proteins
In Silico Biology (2004) 4, 181-186
LocPred Protein Blocks prediction (Bayesian approach).

^*: authors contribute equally. ^#: corresponding author(s).

Alexandre G. de Brevern
Last Modification : August 2017