TRAPP

TRAPP (TRAnsient Pockets in Proteins) is a web-based or stand-alone tool to analyze and detect transient protein subpockets. The TRAPP algorithm includes functions for examining binding site motion, binding site dynamics in various trajectories, detection of transient pockets, binding pocket druggability analysis, analysis, visualization, tracking, and analyses of physicochemical properties.

Topic

Protein binding sites;DNA binding sites;Molecular dynamics

Detail

  • Operation: Protein binding site prediction;Peak calling;Protein flexibility and motion analysis

  • Software interface: Web user interface

  • Language: Java

  • License: EUROPEAN UNION PUBLIC LICENCE v. 1.2.

  • Cost: Free

  • Version name: 4.0.1

  • Credit: Klaus Tschira Foundation, EU-EFPIA Innovative Medicines Initiative (IMI) Joint Undertaking, K4DD; European Union Seventh Framework Programme for research, technological development and demonstration(NMTrypl New Medicines for Trypanosomatidic Infections), HITS gGmbH.

  • Input: PDB, FASTA

  • Output: -

  • Contact: Rebecca C Wade rebecca.wade@h-its.org, Daria B Kokh Daria.Kokh@h-its.org

  • Collection: -

  • Maturity: Stable

Publications

  • TRAPP: a tool for analysis of transient binding pockets in proteins
  • Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC. TRAPP: a tool for analysis of transient binding pockets in proteins. J Chem Inf Model. 2013 May 24;53(5):1235-52. doi: 10.1021/ci4000294. Epub 2013 May 16. PMID: 23621586.
  • https://doi.org/10.1021/ci4000294
  • PMID: 23621586
  • PMC: -
  • TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.
  • Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC. TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Res. 2017 Jul 3;45(W1):W325-W330. doi: 10.1093/nar/gkx277. PMID: 28431137; PMCID: PMC5570179.
  • https://doi.org/10.1093/NAR/GKX277
  • PMID: 28431137
  • PMC: PMC5570179

Download and documentation

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