3D-SURFER: Software for high-throughput protein surface comparison and analysis

Bioinformatics

Volumn 25, Issue 21, 2009, Pages 2843-2844

  La, David ^a   Esquivel Rodríguez, Juan ^b   Venkatraman, Vishwesh ^a   Li, Bin ^b   Sael, Lee ^b   Ueng, Stephen ^b   Ahrendt, Steven ^a   Kihara, Daisuke ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; ELECTRIC POTENTIAL; HIGH THROUGHPUT SCREENING; HYDROPHOBICITY; INFORMATION SERVICE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS; SURFACE PROPERTY;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; SURFACE PROPERTIES;

EID: 70350697850     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp542     Document Type: Article

References (12)

1. Barber,C.B. et al. (1996) The Quickhull algorithm for convex hulls. ACM Trans. Math. Softw., 22, 469-483.
2. Bustos,B. et al. (2007) Content-based 3D object retrieval. IEEE Comput. Graph. Appl., 27, 22-27.
3. Connolly,M.L. (1993) The molecular surface package. J. Mol. Graph. 11, 139-141.
4. Fischer,D. et al. (1993) Surface motifs by a computer vision technique: Searches, detection, and implications for protein-ligand recognition. Proteins, 16, 278-292.
5. Li,B. et al. (2008) Characterization of local geometry of protein surfaces with the visibility. Proteins, 71, 670-683.
6. Orengo,C.A. et al. (2002) The CATH protein family database: A resource for structural and functional. Proteomics, 2, 11-21.
7. Rosen,M. et al. (1998) Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng., 11, 263-277.
8. Sael,L. et al. (2008) Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins, 72, 1259-1273.
9. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
10. Venkatraman,V. et al. (2009) Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Cell Biochem. Biophys., 54, 23-32.
11. Yang,J.M. and Tung,C.H. (2006) Protein structure database search and evolutionary classification. Nucleic Acids Res., 34, 3646-3659.
12. Yeh,J.S. et al. (2005) A web-based three-dimensional protein retrieval system by matching visual. Bioinformatics, 21, 3056-3057.