Richard Friesner

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. doi request reprint Computational methods for high resolution prediction and refinement of protein structures
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, NY, USA
    Curr Opin Struct Biol 23:177-84. 2013
  2. ncbi request reprint A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation
    Thomas F Hughes
    Columbia University, Department of Chemistry, New York, NY 10027, USA
    Phys Chem Chem Phys 14:7724-38. 2012
  3. ncbi request reprint Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    Annu Rev Phys Chem 56:389-427. 2005
  4. pmc Ab initio quantum chemistry: methodology and applications
    Richard 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
  5. ncbi request reprint Quantum mechanical calculations on biological systems
    R A Friesner
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    Curr Opin Struct Biol 8:257-62. 1998
  6. ncbi request reprint Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    J Med Chem 49:6177-96. 2006
  7. ncbi request reprint Large-scale ab initio quantum chemical calculations on biological systems
    R 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
  8. ncbi request reprint Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
  9. ncbi request reprint Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set
    V A Eyrich
    Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY, 10027, USA
    J Mol Biol 288:725-42. 1999
  10. pmc Integrated Modeling Program, Applied Chemical Theory (IMPACT)
    Jay L Banks
    Schrodinger, Inc, New York, NY 10036, USA
    J Comput Chem 26:1752-80. 2005

Research Grants

  1. THEORECTICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2002
  2. THEORETICAL STUDIES OF PROTEIN FOLDING
    Richard Friesner; Fiscal Year: 2003
  3. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2006
  4. THEORETICAL STUDIES OF PROTEIN FOLDING
    Richard Friesner; Fiscal Year: 2007
  5. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2007
  6. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2009
  7. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 1993
  8. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 1990
  9. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard A Friesner; Fiscal Year: 2010

Collaborators

Detail Information

Publications70

  1. doi request reprint Computational methods for high resolution prediction and refinement of protein structures
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, NY, USA
    Curr Opin Struct Biol 23:177-84. 2013
    ..The methodology offers the promise of addressing the refinement problem in homology modeling if an approach can be devised to handle delocalized errors in the structure...
  2. ncbi request reprint A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation
    Thomas 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...
  3. ncbi request reprint Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    Richard 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...
  4. pmc Ab initio quantum chemistry: methodology and applications
    Richard 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...
  5. ncbi request reprint Quantum mechanical calculations on biological systems
    R 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...
  6. ncbi request reprint Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    Richard 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...
  7. ncbi request reprint Large-scale ab initio quantum chemical calculations on biological systems
    R 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...
  8. ncbi request reprint Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard 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...
  9. ncbi request reprint Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set
    V 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...
  10. pmc Integrated Modeling Program, Applied Chemical Theory (IMPACT)
    Jay L Banks
    Schrodinger, Inc, New York, NY 10036, USA
    J Comput Chem 26:1752-80. 2005
    ....
  11. ncbi request reprint Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    Thomas 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...
  12. ncbi request reprint Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach
    Art E Cho
    Center for Biomolecular Simulations, Columbia University, New York, NY 10027, USA
    J Comput Chem 26:915-31. 2005
    ....
  13. ncbi request reprint Flexible ligand docking with Glide
    Matthew 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...
  14. ncbi request reprint Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests
    George 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...
  15. ncbi request reprint PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
    Steven L Dixon
    Schrodinger, Inc, 120 W 45th St, 29th Floor, New York, NY 10036, USA
    J Comput Aided Mol Des 20:647-71. 2006
    ....
  16. pmc Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    Robert Abel
    Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
    J Am Chem Soc 130:2817-31. 2008
    ....
  17. ncbi request reprint High-resolution prediction of protein helix positions and orientations
    Xin 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...
  18. pmc Replica exchange with solute tempering: a method for sampling biological systems in explicit water
    Pu 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...
  19. pmc Serial replica exchange
    Morten 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...
  20. ncbi request reprint Computational modeling of the catalytic reaction in triosephosphate isomerase
    Victor 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...
  21. pmc Dewetting transitions in protein cavities
    Tom 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...
  22. pmc Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    Tom 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...
  23. ncbi request reprint Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase
    Victor Guallar
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    J Am Chem Soc 124:3377-84. 2002
    ....
  24. ncbi request reprint Novel procedure for modeling ligand/receptor induced fit effects
    Woody Sherman
    Schrodinger, 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...
  25. pmc What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules
    Zhiyun Yu
    Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
    J Comput Chem 27:72-89. 2006
    ....
  26. ncbi request reprint On the role of the crystal environment in determining protein side-chain conformations
    Matthew P Jacobson
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    J Mol Biol 320:597-608. 2002
    ....
  27. ncbi request reprint Quantum chemical studies of methane monooxygenase: comparision with P450
    Victor 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...
  28. pmc Computational prediction of native protein ligand-binding and enzyme active site sequences
    Raj 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...
  29. ncbi request reprint A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations
    George 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...
  30. pmc Protein side-chain dynamics and residual conformational entropy
    Nikola 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...
  31. pmc Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions
    Dahlia 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...
  32. pmc Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability
    Byungchan 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...
  33. ncbi request reprint Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques
    Benjamin 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...
  34. pmc Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study
    David 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...
  35. pmc Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450
    Victor 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
    ....
  36. ncbi request reprint Mechanistic studies on the hydroxylation of methane by methane monooxygenase
    Mu Hyun Baik
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    Chem Rev 103:2385-419. 2003
  37. ncbi request reprint Dioxygen activation in methane monooxygenase: a theoretical study
    Benjamin 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
    ....
  38. ncbi request reprint Reversible dioxygen binding to hemerythrin
    Maria 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...
  39. pmc Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations
    Severin 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...
  40. ncbi request reprint A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction scheme
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, NY 10025, USA
    J Chem Phys 125:124107. 2006
    ....
  41. ncbi request reprint Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
    Xin Li
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    Proteins 66:824-37. 2007
    ....
  42. ncbi request reprint Long loop prediction using the protein local optimization program
    Kai 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...
  43. pmc Sequence optimization and designability of enzyme active sites
    Raj 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
    ....
  44. pmc Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation
    Nikola 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...
  45. pmc Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures
    Lingle 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...
  46. pmc Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins
    Paul 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...
  47. pmc Replica exchange with solute tempering: efficiency in large scale systems
    Xuhui 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...
  48. ncbi request reprint A novel fold recognition method using composite predicted secondary structures
    Yuling 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...
  49. ncbi request reprint Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C beta-lactamase
    Benjamin 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...
  50. pmc Density functional localized orbital corrections for transition metals
    David 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...
  51. ncbi request reprint Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study
    Victor 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...
  52. ncbi request reprint 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...
  53. ncbi request reprint Localized orbital corrections for the calculation of ionization potentials and electron affinities in density functional theory
    Eric 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
    ....
  54. ncbi request reprint 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...
  55. ncbi request reprint Kinetics and thermodynamics of H. transfer from (eta5-C5R5)Cr(CO)3H (R = Ph, Me, H) to methyl methacrylate and styrene
    Lihao 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...
  56. ncbi request reprint Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q
    Mu Hyun Baik
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    J Am Chem Soc 124:14608-15. 2002
    ....
  57. pmc Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models
    Lingle 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...
  58. ncbi request reprint Reactions of methane monooxygenase intermediate Q with derivatized methanes
    Edna 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...
  59. ncbi request reprint 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
    ....
  60. pmc Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling
    Jennifer 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...
  61. pmc An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data
    Sarel 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
    ....
  62. pmc Prediction of side-chain conformations on protein surfaces
    Zhexin 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...
  63. ncbi request reprint Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction
    Michael 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
    ....
  64. pmc Toward better refinement of comparative models: predicting loops in inexact environments
    Benjamin 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...
  65. ncbi request reprint A hierarchical approach to all-atom protein loop prediction
    Matthew P Jacobson
    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143 2240, USA
    Proteins 55:351-67. 2004
    ....
  66. pmc The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study
    Ahmet Altun
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, D 45470 Mulheim an der Ruhr, 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...
  67. pmc Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets
    Zhiyong 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...
  68. ncbi request reprint Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery
    Victor 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...
  69. pmc Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study
    Krishna 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...
  70. ncbi request reprint 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
    ....

Research Grants30

  1. THEORECTICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2002
    ..abstract_text> ..
  2. THEORETICAL STUDIES OF PROTEIN FOLDING
    Richard Friesner; Fiscal Year: 2003
    ..abstract_text> ..
  3. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2006
    ..abstract_text> ..
  4. THEORETICAL STUDIES OF PROTEIN FOLDING
    Richard Friesner; Fiscal Year: 2007
    ..Specific biological applications of the methods will involve homology modeling of pharmaceutically interesting targets, such as kinases. ..
  5. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2007
    ..abstract_text> ..
  6. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard Friesner; Fiscal Year: 2009
    ....
  7. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard 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...
  8. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard 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...
  9. THEORETICAL STUDIES OF METALLOPROTEIN CHROMOPHORES
    Richard A Friesner; Fiscal Year: 2010
    ....