PocketPicker: analysis of ligand binding-sites with shape descriptors

[1]  M. Schroeder,et al.  LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation , 2006, BMC Structural Biology.

[2]  K. Sharp,et al.  Travel depth, a new shape descriptor for macromolecules: application to ligand binding. , 2006, Journal of molecular biology.

[3]  Jean-Christophe Nebel,et al.  Generation of 3D templates of active sites of proteins with rigid prosthetic groups , 2006, German Conference on Bioinformatics.

[4]  J. Thornton,et al.  A method for localizing ligand binding pockets in protein structures , 2005, Proteins.

[5]  R. Abagyan,et al.  Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes* , 2005, Molecular & Cellular Proteomics.

[6]  Janet M. Thornton,et al.  Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons , 2005, Bioinform..

[7]  N. Ben-Tal,et al.  The ConSurf‐HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures , 2004, Proteins.

[8]  Gerhard Klebe,et al.  Probing flexibility and “induced‐fit” phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations , 2004, Proteins.

[9]  A. Joachimiak,et al.  Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding , 2004, Cellular and Molecular Life Sciences CMLS.

[10]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[11]  S. J. Campbell,et al.  Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.

[12]  G. Klebe,et al.  Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. , 2002, Farmaco.

[13]  P. Dean,et al.  Recent advances in structure-based rational drug design. , 2000, Current opinion in structural biology.

[14]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[15]  Gerhard Klebe,et al.  Recent developments in structure-based drug design , 2000, Journal of Molecular Medicine.

[16]  G Schneider,et al.  Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network. , 2000, Protein engineering.

[17]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

[18]  W. Thurston Shapes of polyhedra and triangulations of the sphere , 1998, math/9801088.

[19]  M Hendlich,et al.  LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.

[20]  M. Swindells,et al.  Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.

[21]  C. Frömmel,et al.  The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. , 1996, Journal of molecular biology.

[22]  R. Laskowski SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.

[23]  Herbert Edelsbrunner,et al.  Measuring proteins and voids in proteins , 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

[24]  Ernst P. Mücke,et al.  Three-dimensional alpha shapes , 1994, TOGS.

[25]  G J Kleywegt,et al.  Detection, delineation, measurement and display of cavities in macromolecular structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[26]  D. Levitt,et al.  POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. , 1992, Journal of molecular graphics.

[27]  Franz Aurenhammer,et al.  Voronoi diagrams—a survey of a fundamental geometric data structure , 1991, CSUR.

[28]  Chris M. W. Ho,et al.  Cavity search: An algorithm for the isolation and display of cavity-like binding regions , 1990, J. Comput. Aided Mol. Des..

[29]  D. T. Lee,et al.  Two algorithms for constructing a Delaunay triangulation , 1980, International Journal of Computer & Information Sciences.

[30]  R. Abagyan,et al.  Comprehensive identification of "druggable" protein ligand binding sites. , 2004, Genome informatics. International Conference on Genome Informatics.

[31]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[32]  E. Saff,et al.  Distributing many points on a sphere , 1997 .

[33]  H. Berman,et al.  Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .