Richard A. Friesner
Department of Chemistry
3000 Broadway, mail code 3110
New York , NY 10027

work : +1 212-854-7606
fax : +1 212-854-7454

Friesner Group

2005 - 2008 Publications


Edward Harder, Byungchan Kim, Richard A. Friesner and B.J. Berne, Efficient simulation method for polarizable protein force fields: Application to the simulation of BPTI in liquid water, J. Chem. Theory and Comput.  1, 169-180 (2005).
217. Gherman, Benjamin F., Stephen J. Lippard and Richard A. Friesner, Substrate Hydroxylation in Methane Monooxygenase:  Quantitative Modeling via Mixed Quantum Mechanics/Molecular Mechanics Techniques, J. Am. Chem. Soc., 127, 3, 1025 -1037 (2005). 
218. Friesner, Richard A. and Victor Guallar, Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis, Ann. Rev. Phys. Chem., 56, 389-427 (2005).
219. Kaminski, George, A. Jon Maple, Robert B. Murphy, Dale A. Braden, and Richard A. Friesner, Pseudospectral Local Second Order Moller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs, J. Chem. Theo. and Comput., 1, 248-254 (2005).
220. Cho, Art E., Victor Guallar, Bruce J. Berne and Richard Friesner, Importance of Accurate Charges in Molecular Docking:  Quantum Mechanical/Molecular Mechanical (QM/MM) Approach, J. Comp. Chem., 26, 9, 915-931 (2005).
221. Friesner, Richard A., Chemical Theory & Computations Special Feature: Ab Initio Quantum Chemistry: Methodology and Applications, PNAS, 102, 19, 6648-6653, (2005).
222. Zhou, Z. Y.; M. L. Steigerwald, R.A. Friesner, L. Brus, M.S. Hybertsen, Structural and chemical trends in doped silicon nanocrystals: First-principles calculations. Phys. Rev. B, 71, 24, 245308 (2005).
223. Cao, Yixiang, Richard A. Friesner, Molecular (hyper) polarizabilities computed by pseudospectral methods. J Chem. Phys. 122, 10. 104102. (2005). `
224. Kim, Byungchan, Tom Young, Edward Harder, Richard A. Friesner, and Bruce J. Berne, Structure & Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water:  A Comparative Study of the Effects of Solvent and Protein Polarizability,  J. Phys. Chem. B. 109, 34, 16529-16538. (2005). 
225. Pu Liu, Byungchan Kim, Richard A. Friesner, and B. J. Berne, Replica exchange with solute tempering:  A method for sampling biological systems in explicit water.  PNAS, 102, 39, 13749-13754.  (2005).
226. Zhiyong Zhou, Michael L. Steigerwald, Richard A. Friesner, Louis Brus, and Mark S. Hybertsen, Dopant local bonding and electric activity near Si(100)-oxide Interfaces, J. App. Phys., 98, 076105, (2005).    
227. Raj Chakrabarti, Alexander M. Klibanov, Richard A. Friesner, Computational prediction of native protein ligand-binding and enzyme active site sequences, Proc. Nat. Acad. Sci, 102, 29, 10153-10158 (2005).
228. Raj Chakrabarti, Alexander M. Klibanov and Richard A. Friesner, Sequence optimization and designability of enzyme active sites, Proc. Nat. Acad. Sci. USA, 102, 34, 12035-12040, (2005). 
229. Cao, Y.X, M.D. Beachy, D.A. Braden, L. Morrill, M.N. Ringdalda, and R.A. Friesner, Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods, J. Chem. Phys., 122, 22, 224116 (2005).
230. Jovanovic, Tijan, Ramy Farid, Richard A. Friesner and Ann E. McDermott, Thermal Equilibrium of High- and Low- Spin Forms of Cytochrome P450 BM3: Repositioning of the Substrate?  J. Am. Chem. Society, 127, 39, 13548-13552 (2005).
231. Maple, Jon R., Yixiang Cao, Wolfgang Damm, Thomas A. Halgren, George A. Kaminski, Linda Y. Zhang, and Richard A. Friesner, A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions, J. Chem. Theory and Comput, 1, 4, 694-715 (2005).
232. Banks, Jay L., Hege S. Beard, Yixiang Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio and Ronald M. Levy, Integrated Modeling Program, Applied Chemical Theory (IMPACT), J. Comput. Chem., 26, 1752-1780 (2005).
233. Vargas, Rubicelia, Jorge Garza, Richard A. Friesner, Harry Stern, Benjamin P. Hay, and David A. Dixon, Reply to Comment on “Strength of the N-H×××O═C Bonds in Formamide and N-Methylacetamide Dimers,” J. Phys. Chem. A, 109, 6991-6992 (2005).  
234. Sherman, Woody, Tyler Day, Matthew P. Jacobson, Richard A. Friesner, and Ramy Farid, Novel Procedure for Modeling Ligand/Receptor Induced fit Effects, J. Med. Chem., 49, 534-553 (2006).
235. Yu, Zhiyun, Matthew P. Jacobson, and Richard A. Friesner, What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules, J. Comput. Chem., 27 (1): 72-89 (2006)
236. Altun, A, Victor Guallar, Richard A. Friesner, et al., The effect of heme environment on the hydrogen abstraction reaction of camphor in P450(cam) catalysis: A QM/MM study, J. Am. Chem. Soc., 128 (12): 3924-3925 (2006).
237. Farid, Ramy, Tyler Day, Richard A. Friesner, and Robert A. Pearlstein, New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies, Bioorg. Med., Chem., 14 (9): 3160-3173 (2006).
238. Guallar, Victor, Andrzej A. Jarzecki, Richard A. Friesner, and Thomas G. Spiro, Modeling of Ligation-Induced Helix/Loop Displacements in Myoglobin:  Toward an Understanding of Hemoglobin Allostery, J. Am. Chem. Soc., 128, 16, 5427-5435 (2006).  
239. Ravindranathan, Krishna Pratap, Emilio Gallicchio, Richard A. Friesner, Ann E. McDermott, and Ronald M. Levy,Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study, J. Am. Chem. Soc., 128, 17, 5786-5791 (2006).   
240. Friesner, Richard A., Modeling polarization in proteins and protein-ligand complexes: Methods and preliminary results, Peptide Solvation and H-Bonds, Advances in Protein Chemistry, 72, 79 -+ (2006).   
241. Zhu, Kai, David L. Pincus, Suwen Zhao, and Richard A. Friesner, Long Loop Prediction Using the Protein Local Optimization Program, Proteins, Structure, Function and Bioinformatics,  65, 2, 438-452 (2006).   
242. Dixon , Steven L., Alexander M. Smondyrev, Eric H. Knoll, Shashidhar N. Rao, David E. Shaw, Richard A. Friesner, PHASE:  a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening:  1.  Methodology and Preliminary results, J. Computer. Aided Mol. Des., 20, 10-11, 647-671 (2006).   
243. Tang, Lihao H., Elizabeth T. Papish, Graham P. Abramo, Jack R. Norton, Mu-Hyun Baik, Richard A. Friesner, and Anthony Rappe, Kinetics and thermodynamics of H center dot transfer from (eta(5)-C5R5)Cr(CO)(3)H (R = Ph, Me, H) to methyl methacrylate and styrene (vol 125, pg 10093, 2003), J. Am. Chem. Soc., 128, 34, 11314-11314, (2006). 
244. Knoll, Eric H., and Richard A. Friesner, Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory, J. Phys. Chem. B, 110, 38, 18787-18802 (2006).   
245. Friesner, Richard A., Kenneth D. Jordan, and David R. Reichman, Tribute to Robert J. Silbey, J. Phys. Chem. B., 110 (38): 18734-+ (2006).
246. Friesner, Richard A., Eric H. Knoll, Yixiang Cao, and Schrodinger, Inc., A Localized Orbital Analysis of the Thermochemical Errors in Hybrid Density Functional Theory:  Achieving Chemical Accuracy via a Simple Empirical Correction Scheme, J. Chem. Phys., 125, 12, 124107 (2006).    
247. Friesner, Richard A., Robert B. Murphy, Matthew P. Repasky, Leah L. Frye, Jeremy R. Greenwood, Thomas A. Halgren, Paul C. Sanschagrin, Daniel T. Mainz, Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes, J. Med. Chem., 49, 21, 6177-6196 (2006).   
248. Young, Tom, Robert Abel, Byungchan Kim, Bruce J. Berne, and Richard A. Friesner, Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding, Proc. Nat. Acad. Sci., 104, 3, 808-813, (2007). 
249. Hagen, Morten), Byungchan Kim, Pu Liu, Richard A. Friesner, and Bruce J. Berne, Serial replica exchange, J. Phys. Chem. B., 111, 6, 1416-1423 (2007).
250. Xiang, Zhexin, Peter J. Steinbach, Matthew P. Jacobson, Richard A. Friesner, and Barry Honig, Prediction of side-chain conformations on protein surfaces, Prot., Struc. Func. Bioinfor., 66, 4, 814-823 (2007).
251. Li, Xin, Matthew P. Jacobson, Kai Zhu, Suwen Zhao, and Richard A. Friesner, Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling 
Prot. Struc. Func. Bioinfor., 66, 4, 824-837, (2007).
252. Zhu, Kai, Michael R. Shirts, Richard A. Friesner, and Matthew P. Jacobson, Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes, J. Chem. Theor. Comput., 3, 2, 640-648 (2007).
253. Rinaldo, David, Dean M. Philipp, Stephen J. Lippard, and Richard A. Friesner, Intermediates in Dioxygen Activation by Methane Monooxygenase: A QM/MM Study.  J. Am. Chem. Soc., 129, 11, 3135-3147 (2007).
254. Xuhui Huang, Morten Hagen, Byuncghan Kim, Richard A. Friesner, Ruhong Zhou, and Bruce J. Berne, Replica Exchange with Solute Tempering:  Efficiency in Large Scale Systems, J. Phys. Chem. B., 111, 19, 5405-5410 (2007). 
255. Zhou, Zhiyong, Anthony K. Felts, Richard A. Friesnre, and Ronald M. Levy, Comparative performance of several Flexible Docking Programs anbdScoring Functions:  Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets, J. Chem. Inf. Model., 47, 4, 1599-1608 (2007).
256. Kai Zhu, Michael Shirts, Richard Friesner, Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects, J. Chem. Theor. Comput., 3, 6, 2108-2119, (2007).
257. Robert Abel, Tom Young, Ramy Farid , Bruce J. Berne, and Richard A. Friesner, Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding, J. Med. Chem., 130, 9, 2817-2831 (2008).
258. Bochevarov, Arteum D., and Richard A. Friesner, The densities produced by the density functional theory: Comparison to full configuration interaction, J. Chem. Phys., 128, 3, 034102 (2008).
259. Ko, Chaehyuk, David K. Malick, Dale A. Braden, Richard A. Friesner and Todd J. Martinez, Pseudospectral time-dependent density functional theory, J. Chem. Phys., 128, 10, 104103, (2008).
260. Knight, Jennifer L., Zhiyong Zhou, Emilio Gallicchio, Daniel M. Himmel, Richard A. Friesner, Eddy Arnold, and Ronald M. Levy, Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling, Acta Crystallographica Sect. D, Biological Crystallography, 64, 4, 383-396 (2008).
261. Sellers, Benjamin D., Kai Zhu, Suwen Zhao, Richard A. Friesner, Matthew P. Jacobson, Towards better refinement of comparative models:  Predicting loops in inexact environments, Proteins, Structure, Function and Bioinformatics, 72, 3, 959-971 (2008).
262. Maragakis, Paul, Kresten Lindorff-larsen, Michael P. Eastwood, Ron O. Drorr, John L. Klepeis, Isaiah T. Arkin, Morten O. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arther G. Palmer III, and David E. Shaw, Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins, J. Phys. Chem. B, 112, 19, 6156-6158 (2008).
263. Trbovic, Nikola, Byungchan Kim, Richard A. Friesner, and Arthur G. Palmer, III, Structural Analysis of Protein Dynamics by MD Simulations and NMR Spin Relaxation, Proteins, Structure, Function, and Bioinformatics, 71, 2, 684-694 (2008).
264.  Felts, Anthony, K., Emilio Gallicchio, Dmitriy Chekmarev, Kristina A. Paris, Richard A. Friesner, and  Ronald M. Levy, Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling, J. Chem. Theo. Comput., 4, 5, 855-868 (2008).
 265.  Rinaldo, David, Li Tian, Jeremy N. Harvey, and Richard A. Friesner, Density Functional Localized Orbital Corrections for Transition Metals, J. Chem. Phys., 129, 164108-164123 (2008).
 266.  Goldfeld, Dahlia A., Arteum D. Bochevarov, and Richard A. Friesner, Localized orbital corrections applied to thermochemical errors in density functional theory:  The role of basis set and application to molecular reactions, J. Chem. Phys., 129, 21, 214105 (2008).