Papers+Conferences

2003
Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter KH, Vajda S.  2003.  Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. Journal of Molecular Biology. 332(5):1095-1113. Download: PDF (1.9 MB)
Kortvelyesi T, Dennis S, Silberstein M, Brown L, Vajda S.  2003.  Algorithms for computational solvent mapping of proteins. Proteins: Structure, Function, and Genetics. 51(3):340-351. Download: PDF (220.47 KB)
Kortvelyesi T, Silberstein M, Dennis S, Vajda S.  2003.  Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design. 17(2/4):173-186. Download: PDF (397.37 KB)
2002
Dennis S, Vajda S.  2002.  Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. Journal of Computational Chemistry. 23(3):319-334. Download: PDF (1.58 MB)
Dennis S, Kortvelyesi T, Vajda S.  2002.  Computational mapping identifies the binding sites of organic solvents on proteins. Proceedings of the National Academy of Sciences. 99(7):4290-4295. Download: PDF (156.98 KB)
2000
Gatchell DW, Dennis S, Vajda S.  2000.  Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins: Structure, Function, and Genetics. 41(4):518-534. Download: PDF (554.3 KB)
Dennis S, Camacho CJ, Vajda S.  2000.  Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins: Structure, Function, and Genetics. 38(2):176-188. Download: PDF (232.57 KB)
Dennis S, Camacho CJ, Vajda S.  2000.  Exploring potential solvation sites of proteins by multistart local minimization. Optimization in Computational Chemistry and Molecular Biology. :243-261. Download: PDF (289.95 KB)