Alexandre G. de Brevern's Tools
Please find here links to some of my developments.

Protein Superimposition

  1. 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).

  2. 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).

  3. 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.

  4. 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).

  5. 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).

  6. 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

  1. 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.

  2. 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.

  3. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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:W373–378.
    VLDP Amino acid volumes, accessibility and contact determination.

  5. 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

  1. 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.

  2. 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.

  3. 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) 145–153.
    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.

  4. 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.

  5. 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.

  6. 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
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