VASP

VASP (Volumetric Analysis of Surface Properties) is a software tool to compare protein binding sites in alignments. The VASP algorithm uses solid volumes to characterize protein shapes, surface cavities, apertures, and tunnels. The package includes the VASP-E (Volumetric Analysis of Surface Properties with Electrostatics) tool for comparing volumetrics of protein-ligand/protein binding sites using electrostatics.

Topic

Protein structural motifs and surfaces;Protein folds and structural domains

Detail

  • Operation: Molecular surface calculation;Scaffolding;Protein-ligand docking

  • Software interface: Command-line user interface

  • Language: C++;C

  • License: GNU GENERAL PUBLIC LICENSE Version 3

  • Cost: Free

  • Version name: -

  • Credit: National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: Brian Y. Chen chen@cse.lehigh.edu, vasp.materialphysik@univie.ac.at, Barry Honig bh6@columbia.edu

  • Collection: -

  • Maturity: -

Publications

  • VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.
  • Chen BY, Honig B. VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Comput Biol. 2010 Aug 12;6(8):e1000881. doi: 10.1371/journal.pcbi.1000881. PMID: 20814581; PMCID: PMC2930297.
  • https://doi.org/10.1371/journal.pcbi.1000881
  • PMID: 20814581
  • PMC: PMC2930297

Download and documentation

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