Research Topics
| Richard FriesnerSummaryAffiliation: Columbia University Country: USA Publications
Research Grants
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Detail Information
Publications
A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formationThomas F Hughes
Columbia University, Department of Chemistry, New York, NY 10027, USA
Phys Chem Chem Phys 14:7724-38. 2012..74 ± 3.51 kcal/mol to 0.94 ± 0.68 kcal/mol and corrects the functional's under binding in nearly every case. Several important connections among DBLOC parameters have been made...- Quantum mechanical calculations on biological systemsR A Friesner
Department of Chemistry, Columbia University, New York, NY 10027, USA
Curr Opin Struct Biol 8:257-62. 1998..An important direction is the development and application of hybrid quantum chemical-molecular mechanics methods... - Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysisRichard A Friesner
Department of Chemistry, Columbia University, New York, New York 10027, USA
Annu Rev Phys Chem 56:389-427. 2005..Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects... - Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracyRichard A Friesner
Department of Chemistry, Columbia University, New York, New York 10036, USA
J Med Chem 47:1739-49. 2004..Glide is also found to be more accurate than the recently described Surflex method... - Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexesRichard A Friesner
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Med Chem 49:6177-96. 2006..Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives... - Ab initio quantum chemistry: methodology and applicationsRichard A Friesner
Department of Chemistry, Columbia University, 3000 Broadway, MC 3110, New York, NY 10025, USA
Proc Natl Acad Sci U S A 102:6648-53. 2005..A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly... - Large-scale ab initio quantum chemical calculations on biological systemsR A Friesner
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, 3000 Broadway, Mail Code 3110, New York, New York 10027, USA
Acc Chem Res 34:351-8. 2001..Density functional theory is the method of choice for studying reactive chemistry; investigations of the catalytic cycle of the enzyme methane monooxygenase are reviewed... - Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test setV A Eyrich
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY, 10027, USA
J Mol Biol 288:725-42. 1999..This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands... - Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screeningThomas A Halgren
Schrodinger, L L C, 120 W 45th Street, New York, New York 10036, USA
J Med Chem 47:1750-9. 2004..Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01... - Integrated Modeling Program, Applied Chemical Theory (IMPACT)Jay L Banks
, Inc, New York, NY 10036, USA
J Comput Chem 26:1752-80. 2005.... - Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approachArt E Cho
Center for Biomolecular Simulations, Columbia University, New York, NY 10027, USA
J Comput Chem 26:915-31. 2005.... - Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase testsGeorge A Kaminski
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Comput Chem 23:1515-31. 2002..It can be considered as a solid basis for building a more accurate and complete second-generation model... - PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary resultsSteven L Dixon
Schrodinger, Inc, 120 W 45th St, 29th Floor, New York, NY 10036, USA
J Comput Aided Mol Des 20:647-71. 2006.... - High-resolution prediction of protein helix positions and orientationsXin Li
Department of Chemistry, Columbia University, New York, New York, USA
Proteins 55:368-82. 2004..The helix positions are reproduced with an average backbone RMSD of 0.6 A, while the average backbone RMSD of the complete loop-helix-loop region (i.e., the helix with the surrounding loops, which are also repredicted) is 1.3 A... - Flexible ligand docking with GlideMatthew P Repasky
Schrodinger, L L C, New York, New York, USA
Curr Protoc Bioinformatics . 2007..This unit presents protocols for flexible ligand docking with Glide, optionally including ligand constraints or ligand molecular similarities... - Role of the active-site solvent in the thermodynamics of factor Xa ligand bindingRobert Abel
Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
J Am Chem Soc 130:2817-31. 2008.... - Serial replica exchangeMorten Hagen
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Phys Chem B 111:1416-23. 2007..For proof of concept, we apply the SREM to a single alanine dipeptide molecule in explicit water. We show that the SREM reproduces the thermodynamic and structural properties determined by the REM... - Replica exchange with solute tempering: a method for sampling biological systems in explicit waterPu Liu
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
Proc Natl Acad Sci U S A 102:13749-54. 2005..This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water... - Computational modeling of the catalytic reaction in triosephosphate isomeraseVictor Guallar
Department of Chemistry, Columbia University, New York, NY 10027, USA
J Mol Biol 337:227-39. 2004..Our results are consistent with the available experimental data, and provide an initial picture as to why loop opening when GAP is the product has a higher barrier than when DHAP is the product... - What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomoleculesZhiyun Yu
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
J Comput Chem 27:72-89. 2006.... - Computational prediction of native protein ligand-binding and enzyme active site sequencesRaj Chakrabarti
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
Proc Natl Acad Sci U S A 102:10153-8. 2005..These findings suggest that simple selection pressures may have played a predominant role in determining the sequences of ligand-binding and active sites in proteins... - On the role of the crystal environment in determining protein side-chain conformationsMatthew P Jacobson
Department of Chemistry, Columbia University, New York, NY 10027, USA
J Mol Biol 320:597-608. 2002.... - Novel procedure for modeling ligand/receptor induced fit effectsWoody Sherman
, Inc, New York, New York 10036, USA
J Med Chem 49:534-53. 2006..4 A; the RMSD is < or =1.8 A for 18 of the cases. For the three cases with RMSDs greater than 1.8 A, the core of the ligand is properly docked and all key protein/ligand interactions are captured... - Protein side-chain dynamics and residual conformational entropyNikola Trbovic
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
J Am Chem Soc 131:615-22. 2009..Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding... - A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulationsGeorge A Kaminski
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Comput Chem 24:267-76. 2003..We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas... - Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand bindingTom Young
Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
Proc Natl Acad Sci U S A 104:808-13. 2007..Our analysis elucidates several challenging cases, including the super affinity of the streptavidin-biotin system... - Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactionsDahlia A Goldfeld
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Chem Phys 129:214105. 2008..Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies... - Quantum chemical studies of methane monooxygenase: comparision with P450Victor Guallar
Department of Chemistry, Columbia University, New York, NY 10027, USA
Curr Opin Chem Biol 6:236-42. 2002..For P450CAM, in contrast, the inclusion of the full protein is necessary for an accurate description of the hydrogen atom abstraction... - Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenaseVictor Guallar
Department of Chemistry, University of California, Berkeley, CA 94720, USA
J Am Chem Soc 124:3377-84. 2002.... - Dewetting transitions in protein cavitiesTom Young
Department of Chemistry, Columbia University, New York, NY 10027, USA
Proteins 78:1856-69. 2010..Because such cavities need not desolvate before binding hydrophobic ligands they often exhibit very large binding affinities. This article gives evidence that drying in protein cavities is not unique to Cox-2... - Intermediates in dioxygen activation by methane monooxygenase: a QM/MM studyDavid Rinaldo
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Am Chem Soc 129:3135-47. 2007..A discrepancy remains in our calculation of the Fe-Fe distance in our model of HQ as compared to EXAFS data obtained several years ago, for which we currently do not have an explanation... - Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizabilityByungchan Kim
Department of Chemistry and Center for Bimolecular Simulation, Columbia University, 3000 Broadway, New York, New York 10027, USA
J Phys Chem B 109:16529-38. 2005..We find that the solvating water's relaxation is most affected when both the protein and the water models are polarizable. However, when only one model (or neither) is polarizable, the relaxation is similar regardless of the models used... - Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniquesBenjamin F Gherman
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Am Chem Soc 127:1025-37. 2005..More sophisticated sampling methods will be required to achieve greater accuracy in this aspect of the calculation... - Mechanistic studies on the hydroxylation of methane by methane monooxygenaseMu-Hyun Baik
Department of Chemistry, Columbia University, New York, New York 10027, USA
Chem Rev 103:2385-419. 2003 - Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450Victor Guallar
Department of Chemistry and Center for Biomolecular Simulations, Columbia University, New York, NY 10027, USA
Proc Natl Acad Sci U S A 100:6998-7002. 2003.... - Reversible dioxygen binding to hemerythrinMaria Wirstam
Contribution from the Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Am Chem Soc 125:3980-7. 2003..The protein strain energy for this system is negligible. The calculated total O(2) binding free energy is in good agreement with that derived from the experimental equilibrium constant... - Dioxygen activation in methane monooxygenase: a theoretical studyBenjamin F Gherman
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Am Chem Soc 126:2978-90. 2004.... - Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidationsSeverin T Schneebeli
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Am Chem Soc 131:3965-73. 2009..Our work suggests the possibility of using computational methods not simply to explain organic phenomena, but also to predict them quantitatively... - A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction schemeRichard A Friesner
Department of Chemistry, Columbia University, New York, NY 10025, USA
J Chem Phys 125:124107. 2006.... - Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modelingXin Li
Department of Chemistry, Columbia University, New York, NY 10027, USA
Proteins 66:824-37. 2007.... - Structural analysis of protein dynamics by MD simulations and NMR spin-relaxationNikola Trbovic
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 71:684-94. 2008..Structural analysis reveals that relative imbalance between the description of hydrogen bonding and other terms of modern force fields may be responsible for disagreement... - Long loop prediction using the protein local optimization programKai Zhu
Department of Chemistry, Columbia University, New York, New York 10027, USA
Proteins 65:438-52. 2006..A discussion of these results in the context of the general question of the accuracy of continuum solvation models is presented... - Sequence optimization and designability of enzyme active sitesRaj Chakrabarti
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
Proc Natl Acad Sci U S A 102:12035-40. 2005.... - Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosuresLingle Wang
Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
J Phys Chem B 114:7294-301. 2010..Statistical perturbation theory explains these results and shows when and why implicit solvent models fail... - Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics studyVictor Guallar
Department of Chemistry and Center for Biomolecular Simulations, Columbia University, New York, New York 10027, USA
J Am Chem Soc 126:8501-8. 2004..Our results are consistent with the effect of mutations on the enzymatic efficacy and provide a satisfactory explanation for the experimental failure to trap the proposed catalytically competent species, a ferryl Fe(IV) heme... - Thermal equilibrium of high- and low-spin forms of cytochrome P450 BM-3: repositioning of the substrate?Tijana Jovanovic
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Am Chem Soc 127:13548-52. 2005..With this combination of theory and experiment we provide a specific proposal of how ligands may be positioned for chemistry for this enzyme... - Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteinsPaul Maragakis
D E Shaw Research, New York, New York 10036, USA
J Phys Chem B 112:6155-8. 2008..Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations... - Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C beta-lactamaseBenjamin F Gherman
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Am Chem Soc 126:7652-64. 2004..This work provides an essential foundation for further work in this area, such as selecting mutations capable of converting the PBP into a beta-lactamase... - Density functional localized orbital corrections for transition metalsDavid Rinaldo
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
J Chem Phys 129:164108. 2008..The model was also able to predict an outlier in the experimental data that was further investigated with high level coupled-cluster calculations... - A novel fold recognition method using composite predicted secondary structuresYuling An
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
Proteins 48:352-66. 2002..The program successfully locates homologues with high Z-score and low root-mean-score deviation within the top 30-50 predictions in the overwhelming majority of cases... - Replica exchange with solute tempering: efficiency in large scale systemsXuhui Huang
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Phys Chem B 111:5405-10. 2007..Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper... - Reactions of methane monooxygenase intermediate Q with derivatized methanesEdna A Ambundo
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Am Chem Soc 124:8770-1. 2002..In addition, evidence of a substrate-binding step that occurs prior to substrate oxidation is observed... - Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent modelsLingle Wang
Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
Faraday Discuss 146:247-62; discussion 283-98, 395-401. 2010..We also show how the non-additivity contribution changes as the hydrophobicity of the plate is decreased from the dewetting regime to the wetting regime... - Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate QMu-Hyun Baik
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Am Chem Soc 124:14608-15. 2002.... - Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination?Mu-Hyun Baik
Department of Chemistry, Columbia University, New York, New York 10027, USA
J Am Chem Soc 124:4495-503. 2002.... - Localized orbital corrections for the calculation of ionization potentials and electron affinities in density functional theoryEric H Knoll
Department of Chemistry, Columbia University, Havemeyer Hall, MC 3110, New York, New York 10025, USA
J Phys Chem B 110:18787-802. 2006.... - Kinetics and thermodynamics of H. transfer from (eta5-C5R5)Cr(CO)3H (R = Ph, Me, H) to methyl methacrylate and styreneLihao Tang
Departments of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
J Am Chem Soc 125:10093-102. 2003..5 kcal/mol), and a C-H BDE of 47.9 kcal/mol for the alpha-methylbenzyl radical 4 (close to the DFT-calculated 49.9 kcal/mol). A solvent cage model suggests 46.1 kcal/mol as the C-H BDE for the chain-carrying radical in MMA polymerization... - Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine?Mu Hyun Baik
Department of Chemistry, Columbia University, New York, NY 10027, USA
J Am Chem Soc 125:14082-92. 2003..A detailed MO analysis is presented to provide an intuitive view into the different electronic features governing the character of the Pt-N7 bond in platinated purine bases... - Prediction of side-chain conformations on protein surfacesZhexin Xiang
Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 5624, USA
Proteins 66:814-23. 2007..The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 A, with and without consideration of crystal packing effects, respectively... - A hierarchical approach to all-atom protein loop predictionMatthew P Jacobson
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143 2240, USA
Proteins 55:351-67. 2004.... - An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary dataSarel J Fleishman
Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat-Aviv 69978, Israel
Biophys J 87:3448-59. 2004.... - Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle samplingJennifer L Knight
The Scripps Research Institute, La Jolla, CA 92037, USA
Acta Crystallogr D Biol Crystallogr 64:383-96. 2008..An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates... - Toward better refinement of comparative models: predicting loops in inexact environmentsBenjamin D Sellers
Graduate Group in Biophysics, University of California, San Francisco, California 94158 2517, USA
Proteins 72:959-71. 2008..Although many challenges remain in refining full comparative models to high accuracy, this work offers a methodical step toward that goal... - Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer predictionMichael Andrec
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
J Struct Funct Genomics 2:103-11. 2002.... - The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM studyAhmet Altun
, Kaiser-Wilhelm-Platz 1, , Germany
J Am Chem Soc 128:3924-5. 2006..Spin density at the A-propionate side chain of heme can occur in the case of incomplete screening but has no major effect on the computed barrier... - Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allosteryVictor Guallar
Department of Biochemistry, Washington University School of Medicine, St, Louis, Missouri 63108, USA
J Am Chem Soc 128:5427-35. 2006..A similar EF rotation and CD loop displacement are proposed to be the first steps along the allosteric pathway from the R to the T state in hemoglobin... - Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics studyKrishna Pratap Ravindranathan
Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
J Am Chem Soc 128:5786-91. 2006..We use the temperature weighted histogram (T-WHAM) method to characterize the transition state regions of the conformational ensemble and propose a mechanism of interconversion between these low free energy conformational states... - cis-[Pt(NH3)2(L)]2+/+ (L = Cl, H2O, NH3) binding to purines and CO: does pi-back-donation play a role?Mu Hyun Baik
Department of Chemistry and School of Informatics, Indiana University, Bloomington, Indiana 47405, USA
Inorg Chem 42:8615-7. 2003.... - Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targetsZhiyong Zhou
BioMaPS Institute for Quantitative Biology, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
J Chem Inf Model 47:1599-608. 2007..The study also shows that docking into multiple receptor structures can decrease the docking error in screening a diverse set of active compounds...
Research Grants
- THEORECTICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 2002..abstract_text> ..
- THEORETICAL STUDIES OF PROTEIN FOLDINGRichard Friesner; Fiscal Year: 2003..abstract_text> ..
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 2006..abstract_text> ..
- THEORETICAL STUDIES OF PROTEIN FOLDINGRichard Friesner; Fiscal Year: 2007..Specific biological applications of the methods will involve homology modeling of pharmaceutically interesting targets, such as kinases. ..
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 2007..abstract_text> ..
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 2009....
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 1993..The microscopic simulations described above will allow more quantitative models to be constructed, and will permit confirmation (or contradiction) of the basic picture that we have assembled on the basis of phenomenological modeling...
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard Friesner; Fiscal Year: 1990..Determination of the factors which control electron transport efficiency and ligand binding and the capacity to predict the effects of chemical modifications on these properties should greatly facilitate the drug design process...
- THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORESRichard A Friesner; Fiscal Year: 2010....