Sandor Vajda

Professor
Department of Biomedical Engineering, with joint appointment in the Department of Chemistry

Scientific computing, primarily optimization; computational chemistry and biology, including protein and peptide structure determination, protein engineering, and drug design.

Office: ERB 221
Phone: 617-353-4757
Fax: 617-353-6766
E-mail: vajda@bu.edu

Office hours: By appointment

• Ph.D., Chemistry, Hungarian Academy of Science
• M.Sc., Applied Mathematics, Éötvös Lorand University (Hungary)
• M.Sc., Electrical Engineering, Gubkin Institute (Former USSR)

• 1967 Full International Scholarship (5 years) from the Hungarian State
• 1972 Distinguished Diploma in Electrical Engineering, Gubkin Institute, Moscow, USSR
• 1975 Technical Doctorate in Chemical Engineering, Summa Cum Laude, College for Chemical Industry, Veszprem, Hungary, 5/1975
• 1980 Distinguished Diploma in Applied Mathematics (GPA: 4.92/5.0), Eotvos Lorand University, Budapest, Hungary
• 1985 CNRS (France) Scholarship
• 1986 SERC (UK) Postdoctoral Fellowship

• National Science Foundation
• National Institutes of Health
• Department of Energy
• NATO
• ACS/Petroleum Research Fund

• Introduction to Biomolecular Engineering
• Thermodynamics and Statistical Mechanics
• Molecular and Cellular System Analysis
• Structural Bioinformatics Molecular Bioengineering

The primary goal of Dr. Vajda's research is to develop a methodology that will permit a predictive understanding of ligand recognition by protein receptors. Such understanding is the key to rational drug and vaccine design strategies, and requires the solution of several challenging problems. The problems currently studied include (1) evaluation of binding free energy in protein-ligand complexes; (2) development of efficient docking algorithms that will find structures for the complex at or near the global free energy minimum; (3) computational solvent mapping of proteins using molecular probes - small molecules or functional groups - to identify the most favorable binding positions, (4) design of amino acid mutations to induce certain changes in the affinity and specificity of a binding site. His group considers computational mapping particularly interesting, because mapping results provide detailed and reliable information on the functional sites of proteins, and hence the method is potentially very important for structural genomics and drug design applications.

• Structural Bioimformatics Laboratory

• SELECTION
• Landon MR, Amaro R, Baron R, Ngan C, Ozonoff D, McCammon A, Vajda S. Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble. Chem Biol Drug Des. 2008 Jan 17
• Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. ClusPro: Performance in CAPRI rounds 6-11 and the new server. Proteins. 2007 Sep 17

• Shen Y, Brenke R, Comeau SR, Beglov D, Vajda S. Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI. Proteins. 2007 Sep 17

  Silberstein M. , Damborsky J , Vajda S. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 2007 Jul 24 F

  JC Prasad, JV Goldstone,CJ Camacho, Vajda S and JJ Stegeman. Ensemble Modelling of Substrate Binding to Cytochrome P450: Analysis of Vatalitic Differences between CYP1A Orthologs Biochemistry, 2007 Feb 15

  Landon MR, Lancia DR Jr, Jessamin Yu, Spencer C Thiel and Vajda S. Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins J Med Chem, 2007 Feb 12

  Filiz M. Aslan, Yong Yu, Vajda S, Scott C. Mohr, Charles R. Cantor. Engineering a novel, stable dimeric streptavidin with lower isoelectric point Journal of Biotechnology, 128(2007)213-225

  IC Paschalidis, Yang Shen, Pirooz Vakili , Vajda S . SDU: A Semi-Definite programming based Underestimation method for stochastic global optimizationin protein docking IEEE Transaction of Automatic Control, Vol 52, No.5 May (2007)