Method Development - Computer Vision Based Algorithms

Maizel, Jacob V.

Abstract

To enable the database analysis and the docking, we develop novel, state of-the-art computational tools which are unique in speed and capabilities. These include a sequence order-independent multiple structure alignment routine that simultaneously compares all structures, and finds in around a minute of CPU on a workstation the optimally conserved structural motif; A rapid method for flexible protein structure comparisons with no predefinition of the hinges (in seconds); Rigid-body and hinge-bending docking algorithms which consider entire protein surfaces, and carry out docking in minutes as compared to days by other methods; Develoment of algorithms for finding cavities on protein surfaces; Comparisons of databases of drugs, allowing rotations on covalent bonds.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: Division of Basic Sciences - NCI (NCI)
• Type: Intramural Research (Z01)
• Project #: 1Z01BC010442-01
• Application #: 6753237
• Study Section: (LECB)
• Support Year: 1
• Fiscal Year: 2002

Institution

• Name: Basic Sciences
• Country: United States

Publications

Zanuy, David; Ballano, Gema; Jimenez, Ana I et al. (2009) Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 49:1623-9

Schneidman-Duhovny, Dina; Dror, Oranit; Inbar, Yuval et al. (2008) Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules. J Comput Biol 15:737-54

Yaffe, Eitan; Fishelovitch, Dan; Wolfson, Haim J et al. (2008) MolAxis: efficient and accurate identification of channels in macromolecules. Proteins 73:72-86

Shatsky, Maxim; Shulman-Peleg, Alexandra; Nussinov, Ruth et al. (2006) The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol 13:407-28

Shatsky, Maxim; Nussinov, Ruth; Wolfson, Haim J (2006) Optimization of multiple-sequence alignment based on multiple-structure alignment. Proteins 62:209-17

Wainreb, Gilad; Haspel, Nurit; Wolfson, Haim J et al. (2006) A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly. Bioinformatics 22:1343-52

Dror, Oranit; Nussinov, Ruth; Wolfson, Haim J (2006) The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res 34:W412-5

Wolfson, Haim J; Shatsky, Maxim; Schneidman-Duhovny, Dina et al. (2005) From structure to function: methods and applications. Curr Protein Pept Sci 6:171-83

Mintz, Shira; Shulman-Peleg, Alexandra; Wolfson, Haim J et al. (2005) Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins 61:6-20

Inbar, Yuval; Benyamini, Hadar; Nussinov, Ruth et al. (2005) Prediction of multimolecular assemblies by multiple docking. J Mol Biol 349:435-47