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.
| 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 |
| Schneidman-Duhovny, Dina; Inbar, Yuval; Nussinov, Ruth et al. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-7 |
| Dror, Oranit; Nussinov, Ruth; Wolfson, Haim (2005) ARTS: alignment of RNA tertiary structures. Bioinformatics 21 Suppl 2:ii47-53 |
| Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J (2005) SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res 33:W337-41 |
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