3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

[1]  Yifeng D. Yang,et al.  Multi‐LZerD: Multiple protein docking for asymmetric complexes , 2012, Proteins.

[2]  Bin Li,et al.  Characterization of local geometry of protein surfaces with the visibility criterion , 2008, Proteins.

[3]  Daisuke Kihara,et al.  Protein Binding Ligand Prediction Using Moments-Based Methods , 2011 .

[4]  Tim J. P. Hubbard,et al.  Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..

[5]  Jinn-Moon Yang,et al.  Protein structure database search and evolutionary classification , 2006, Nucleic acids research.

[6]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[7]  Daisuke Kihara,et al.  Improved protein surface comparison and application to low-resolution protein structure data , 2010, BMC Bioinformatics.

[8]  Daisuke Kihara,et al.  Protein-protein docking using region-based 3D Zernike descriptors , 2009, BMC Bioinformatics.

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

[10]  Ultra-potent P1 modified arylsulfonamide HIV protease inhibitors: the discovery of GW0385. , 2006, Bioorganic & medicinal chemistry letters.

[11]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[12]  Daisuke Kihara,et al.  3D-SURFER: software for high-throughput protein surface comparison and analysis , 2009, Bioinform..

[13]  Daisuke Kihara,et al.  Function Prediction of uncharacterized proteins , 2007, J. Bioinform. Comput. Biol..

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

[15]  J. Ferrer,et al.  Catalytic Water Co-Existing with a Product Peptide in the Active Site of HIV-1 Protease Revealed by X-Ray Structure Analysis , 2009, PloS one.

[16]  Daisuke Kihara,et al.  Structure- and sequence-based function prediction for non-homologous proteins , 2012, Journal of Structural and Functional Genomics.

[17]  David P. Dobkin,et al.  The quickhull algorithm for convex hulls , 1996, TOMS.

[18]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[19]  Daisuke Kihara,et al.  Application of 3D Zernike descriptors to shape-based ligand similarity searching , 2009, J. Cheminformatics.

[20]  M L Connolly,et al.  The molecular surface package. , 1993, Journal of molecular graphics.

[21]  M. Hanlon,et al.  Ultra-potent P1 modified arylsulfonamide HIV protease inhibitors: the discovery of GW0385. , 2006, Bioorganic & medicinal chemistry letters.

[22]  D. Kihara,et al.  Detecting local ligand‐binding site similarity in nonhomologous proteins by surface patch comparison , 2012, Proteins.

[23]  Marcin Novotni,et al.  3D zernike descriptors for content based shape retrieval , 2003, SM '03.

[24]  Bing-Yu Chen,et al.  A web-based three-dimensional protein retrieval system by matching visual similarity , 2005, Bioinform..

[25]  Daisuke Kihara,et al.  Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. , 2011, Current protein & peptide science.

[26]  Bin Li,et al.  Fast protein tertiary structure retrieval based on global surface shape similarity , 2008, Proteins.