3V: cavity, channel and cleft volume calculator and extractor

As larger macromolecular structures become available, there is a growing need to understand their ‘internal’ volumes—such as deep clefts, channels and cavities—as these often play critical roles in their function. The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures. It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 Å for water). The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis. The 3V server and source code are available from http://3vee.molmovdb.org.

[1]  M Gerstein,et al.  Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly. , 2005, Journal of Molecular Biology.

[2]  Jaroslav Koca,et al.  CAVER: a new tool to explore routes from protein clefts, pockets and cavities , 2006, BMC Bioinformatics.

[3]  K. Kinoshita,et al.  Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site , 2003, Protein science : a publication of the Protein Society.

[4]  Richard M. Jackson,et al.  Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..

[5]  Jaroslav Koca,et al.  MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. , 2007, Structure.

[6]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

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

[8]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[9]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[10]  T. Steitz,et al.  The kink‐turn: a new RNA secondary structure motif , 2001, The EMBO journal.

[11]  W. Scott,et al.  Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis , 2006, Cell.

[12]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[13]  C. Venkatachalam,et al.  LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.

[14]  Douglas C. Rees,et al.  Structures of the Prokaryotic Mechanosensitive Channels MscL and MscS , 2007 .

[15]  Gabriele Ausiello,et al.  SURFACE: a database of protein surface regions for functional annotation , 2004, Nucleic Acids Res..

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

[17]  K. Sharp,et al.  Finding and characterizing tunnels in macromolecules with application to ion channels and pores. , 2009, Biophysical journal.

[18]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

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

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

[21]  Dario Ghersi,et al.  SITEHOUND-web: a server for ligand binding site identification in protein structures , 2009, Nucleic Acids Res..

[22]  Janet M. Thornton,et al.  PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure , 2009, PLoS Comput. Biol..

[23]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[24]  Yue Weng,et al.  Structure of P-Glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding , 2009, Science.

[25]  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.

[26]  Ruth Nussinov,et al.  MolAxis: a server for identification of channels in macromolecules , 2008, Nucleic Acids Res..

[27]  Yong Zhou,et al.  Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere , 2010, Bioinform..

[28]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[29]  M Gerstein,et al.  The geometry of the ribosomal polypeptide exit tunnel. , 2006, Journal of molecular biology.

[30]  R Diamond,et al.  Real-space refinement of the structure of hen egg-white lysozyme. , 1977, Journal of molecular biology.

[31]  Wen-Hsiung Li,et al.  SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns , 2009, Nucleic Acids Res..

[32]  B. Wallace,et al.  HOLE: a program for the analysis of the pore dimensions of ion channel structural models. , 1996, Journal of molecular graphics.

[33]  Zbyszek Otwinowski,et al.  The crystal structure of the bacterial chaperonln GroEL at 2.8 Å , 1994, Nature.

[34]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .