| Year |
Citation |
Score |
| 2024 |
Yi X, Zhang L, Friesner RA, McDermott A. Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics. The Journal of Physical Chemistry Letters. 15: 2270-2278. PMID 38381862 DOI: 10.1021/acs.jpclett.3c02589 |
0.546 |
|
| 2023 |
Coskun D, Lihan M, Rodrigues JPGLM, Vass M, Robinson D, Friesner RA, Miller EB. Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation. Journal of Chemical Theory and Computation. PMID 38100422 DOI: 10.1021/acs.jctc.3c00839 |
0.807 |
|
| 2023 |
Xu Y, Chen J, Aydt AP, Zhang L, Sergeyev I, Keeler EG, Choi B, He S, Reichman DR, Friesner RA, Nuckolls C, Steigerwald ML, Roy X, McDermott AE. Electron and Spin Delocalization in [Co Se (PEt ) ] Superatoms. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. e202300064. PMID 38057144 DOI: 10.1002/cphc.202300064 |
0.641 |
|
| 2023 |
Weber JL, Vuong H, Friesner RA, Reichman DR. Expanding the Design Space of Constraints in Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. 19: 7567-7576. PMID 37889331 DOI: 10.1021/acs.jctc.3c00654 |
0.498 |
|
| 2023 |
Debnath S, Neufeld VA, Jacobson LD, Rudshteyn B, Weber JL, Berkelbach TC, Friesner RA. Accurate Quantum Chemical Reaction Energies for Lithium-Mediated Electrolyte Decomposition and Evaluation of Density Functional Approximations. The Journal of Physical Chemistry. A. 127: 9178-9184. PMID 37878768 DOI: 10.1021/acs.jpca.3c04369 |
0.698 |
|
| 2023 |
Neugebauer H, Vuong HT, Weber JL, Friesner RA, Shee J, Hansen A. Toward Benchmark-Quality Predictions for 3d Transition Metal Electrocatalysts: A Comparison of CCSD(T) and ph-AFQMC. Journal of Chemical Theory and Computation. PMID 37655473 DOI: 10.1021/acs.jctc.3c00617 |
0.634 |
|
| 2023 |
Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. Journal of Molecular Biology. 435: 168187. PMID 37355034 DOI: 10.1016/j.jmb.2023.168187 |
0.798 |
|
| 2023 |
Chen W, Cui D, Jerome SV, Michino M, Lenselink EB, Huggins DJ, Beautrait A, Vendome J, Abel R, Friesner RA, Wang L. Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 37167486 DOI: 10.1021/acs.jcim.3c00013 |
0.818 |
|
| 2023 |
Shee J, Weber JL, Reichman DR, Friesner RA, Zhang S. On the potentially transformative role of auxiliary-field quantum Monte Carlo in quantum chemistry: A highly accurate method for transition metals and beyond. The Journal of Chemical Physics. 158: 140901. PMID 37061483 DOI: 10.1063/5.0134009 |
0.732 |
|
| 2023 |
Yi X, Zhang L, Friesner RA, McDermott A. Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics. Biorxiv : the Preprint Server For Biology. PMID 36747635 DOI: 10.1101/2023.01.25.525502 |
0.562 |
|
| 2022 |
Coskun D, Chen W, Clark AJ, Lu C, Harder ED, Wang L, Friesner RA, Miller EB. Reliable and Accurate Prediction of Single-Residue p Values through Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation. PMID 36384001 DOI: 10.1021/acs.jctc.2c00954 |
0.803 |
|
| 2022 |
Xu T, Zhu K, Beautrait A, Vendome J, Borrelli KW, Abel R, Friesner RA, Miller EB. Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models. Journal of Chemical Theory and Computation. PMID 35972903 DOI: 10.1021/acs.jctc.2c00371 |
0.656 |
|
| 2022 |
Dajnowicz S, Agarwal G, Stevenson JM, Jacobson LD, Ramezanghorbani F, Leswing K, Friesner RA, Halls MD, Abel R. High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations. The Journal of Physical Chemistry. B. PMID 35972463 DOI: 10.1021/acs.jpcb.2c03746 |
0.506 |
|
| 2022 |
Weber JL, Vuong H, Devlaminck PA, Shee J, Lee J, Reichman DR, Friesner RA. A Localized-Orbital Energy Evaluation for Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 35507769 DOI: 10.1021/acs.jctc.2c00111 |
0.719 |
|
| 2022 |
Rudshteyn B, Weber JL, Coskun D, Devlaminck PA, Zhang S, Reichman DR, Shee J, Friesner RA. Calculation of Metallocene Ionization Potentials via Auxiliary Field Quantum Monte Carlo: Toward Benchmark Quantum Chemistry for Transition Metals. Journal of Chemical Theory and Computation. PMID 35377642 DOI: 10.1021/acs.jctc.1c01071 |
0.809 |
|
| 2021 |
Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. Journal of Chemical Theory and Computation. PMID 34096718 DOI: 10.1021/acs.jctc.1c00302 |
0.512 |
|
| 2021 |
Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, ... Friesner RA, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136 |
0.805 |
|
| 2020 |
Weber JL, Churchill EM, Jockusch S, Arthur EJ, Pun AB, Zhang S, Friesner RA, Campos LM, Reichman DR, Shee J. prediction of annihilators for triplet-triplet annihilation upconversion auxiliary-field quantum Monte Carlo. Chemical Science. 12: 1068-1079. PMID 34163873 DOI: 10.1039/d0sc03381b |
0.731 |
|
| 2020 |
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, ... ... Friesner RA, et al. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host & Microbe. PMID 33271067 DOI: 10.1016/j.chom.2020.11.004 |
0.76 |
|
| 2020 |
Zhou T, Tsybovsky Y, Olia AS, Gorman J, Rapp MA, Cerutti G, Katsamba PS, Nazzari A, Schon A, Wang PD, Bimela J, Shi W, Teng IT, Zhang B, Boyington JC, ... ... Friesner RA, et al. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. Biorxiv : the Preprint Server For Biology. PMID 32637958 DOI: 10.1101/2020.07.04.187989 |
0.756 |
|
| 2020 |
Kumar M, Shee J, Rudshteyn B, Reichman DR, Friesner RA, Miller CE, Francisco JS. Multiple Stable Isoprene-Ozone Complexes Reveal Complex Entrance Channel Dynamics in the Isoprene + Ozone Reaction. Journal of the American Chemical Society. PMID 32431151 DOI: 10.1021/Jacs.0C02360 |
0.788 |
|
| 2020 |
Rudshteyn B, Coskun D, Weber JL, Arthur EJ, Zhang S, Reichman DR, Friesner RA, Shee J. Predicting Ligand-Dissociation Energies of 3 Coordination Complexes with Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 32293882 DOI: 10.1021/Acs.Jctc.0C00070 |
0.807 |
|
| 2020 |
Li G, Rudshteyn B, Shee J, Weber JL, Coskun D, Bochevarov AD, Friesner RA. Accurate Quantum Chemical Calculation of Ionization Potentials: Validation of the DFT-LOC Approach via a Large Data Set Obtained from Experiment and Benchmark Quantum Chemical Calculations. Journal of Chemical Theory and Computation. PMID 32150400 DOI: 10.1021/Acs.Jctc.9B00875 |
0.801 |
|
| 2019 |
Shee J, Arthur EJ, Zhang S, Reichman DR, Friesner RA. Singlet-Triplet Energy Gaps of Organic Biradicals and Polyacenes with Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 31381324 DOI: 10.1021/Acs.Jctc.9B00534 |
0.74 |
|
| 2019 |
Shee J, Rudshteyn B, Arthur EJ, Zhang S, Reichman DR, Friesner RA. On Achieving High Accuracy in Quantum Chemical Calculations of 3d Transition Metal-containing Systems: A Comparison of Auxiliary-Field Quantum Monte Carlo with Coupled Cluster, Density Functional Theory, and Experiment for Diatomic Molecules. Journal of Chemical Theory and Computation. PMID 30883110 DOI: 10.1021/Acs.Jctc.9B00083 |
0.815 |
|
| 2019 |
Clark AJ, Negron C, Hauser K, Sun M, Wang L, Abel R, Friesner RA. Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces. Journal of Molecular Biology. PMID 30776430 DOI: 10.1016/J.Jmb.2019.02.003 |
0.804 |
|
| 2019 |
Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 30768902 DOI: 10.1021/Acs.Jctc.8B01026 |
0.575 |
|
| 2018 |
Abel R, Manas ES, Friesner RA, Farid RS, Wang L. Modeling the value of predictive affinity scoring in preclinical drug discovery. Current Opinion in Structural Biology. 52: 103-110. PMID 30321805 DOI: 10.1016/J.Sbi.2018.09.002 |
0.552 |
|
| 2018 |
Shee J, Arthur EJ, Zhang S, Reichman DR, Friesner RA. Phaseless Auxiliary-Field Quantum Monte Carlo on Graphical Processing Units. Journal of Chemical Theory and Computation. PMID 29897748 DOI: 10.1021/Acs.Jctc.8B00342 |
0.735 |
|
| 2017 |
Jacobson LD, Bochevarov AD, Watson MA, Hughes TF, Rinaldo D, Ehrlich S, Steinbrecher TB, Vaitheeswaran S, Philipp DM, Halls MD, Friesner RA. An automated transition state search and its application to diverse types of organic reactions. Journal of Chemical Theory and Computation. PMID 28957627 DOI: 10.1021/Acs.Jctc.7B00764 |
0.326 |
|
| 2017 |
Abel R, Wang L, Harder ED, Berne BJ, Friesner RA. Advancing Drug Discovery through Enhanced Free Energy Calculations. Accounts of Chemical Research. PMID 28677954 DOI: 10.1021/Acs.Accounts.7B00083 |
0.682 |
|
| 2017 |
Shee J, Zhang S, Reichman DR, Friesner RA. Chemical Transformations Approaching Chemical Accuracy via Correlated Sampling in Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 28481546 DOI: 10.1021/Acs.Jctc.7B00224 |
0.752 |
|
| 2017 |
Abel R, Wang L, Mobley DL, Friesner RA. A Critical Review of Validation, Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Current Topics in Medicinal Chemistry. PMID 28413950 DOI: 10.2174/1568026617666170414142131 |
0.608 |
|
| 2017 |
Steinbrecher T, Abel R, Clark A, Friesner R. Perspective: Free energy perturbation calculations of the thermodynamics of protein side chain mutations. Journal of Molecular Biology. PMID 28279701 DOI: 10.1016/J.Jmb.2017.03.002 |
0.599 |
|
| 2017 |
Friesner RA, Jerome SV. Localized orbital corrections for density functional calculations on transition metal containing systems Coordination Chemistry Reviews. 344: 205-213. DOI: 10.1016/J.Ccr.2017.02.014 |
0.8 |
|
| 2016 |
Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Friesner R, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5 |
0.452 |
|
| 2016 |
Wang L, Deng Y, Wu Y, Kim B, LeBard DN, Wandschneider D, Beachy M, Friesner RA, Abel R. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery. Journal of Chemical Theory and Computation. PMID 27933808 DOI: 10.1021/Acs.Jctc.6B00991 |
0.695 |
|
| 2016 |
Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. Journal of Molecular Biology. PMID 27908641 DOI: 10.1016/J.Jmb.2016.11.021 |
0.742 |
|
| 2016 |
Abel R, Mondal S, Masse C, Greenwood J, Harriman G, Ashwell MA, Bhat S, Wester R, Frye L, Kapeller R, Friesner RA. Accelerating drug discovery through tight integration of expert molecular design and predictive scoring. Current Opinion in Structural Biology. 43: 38-44. PMID 27816785 DOI: 10.1016/J.Sbi.2016.10.007 |
0.564 |
|
| 2016 |
Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. Journal of Chemical Theory and Computation. PMID 27145262 DOI: 10.1021/Acs.Jctc.6B00201 |
0.68 |
|
| 2016 |
Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A flexible and accurate treatment of explicit water molecules in ligand-receptor docking. Journal of Medicinal Chemistry. PMID 27054459 DOI: 10.1021/Acs.Jmedchem.6B00131 |
0.812 |
|
| 2016 |
Cao Y, Hughes T, Giesen D, Halls MD, Goldberg A, Vadicherla TR, Sastry M, Patel B, Sherman W, Weisman AL, Friesner RA. Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules. Journal of Computational Chemistry. PMID 27013141 DOI: 10.1002/Jcc.24350 |
0.392 |
|
| 2016 |
Coskun D, Jerome SV, Friesner RA. Evaluation of the performance of the B3LYP, PBE0, and M06 DFT functionals, and DBLOC-corrected versions, in the calculation of redox potentials and spin splittings for transition metal containing systems. Journal of Chemical Theory and Computation. PMID 26808695 DOI: 10.1021/Acs.Jctc.5B00782 |
0.789 |
|
| 2016 |
Zhang J, Weisman AL, Saitta P, Friesner RA. Efficient simulation of large materials clusters using the jaguar quantum chemistry program: Parallelization and wavefunction initialization International Journal of Quantum Chemistry. 116: 357-368. DOI: 10.1002/Qua.25043 |
0.747 |
|
| 2015 |
Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti D, Krilov G, Jorgensen WL, Abel R, ... Friesner RA, et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation. PMID 26584231 DOI: 10.1021/Acs.Jctc.5B00864 |
0.666 |
|
| 2015 |
Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W. Accurate Binding Free Energy Predictions in Fragment Optimization. Journal of Chemical Information and Modeling. PMID 26457994 DOI: 10.1021/Acs.Jcim.5B00538 |
0.605 |
|
| 2015 |
Jerome SV, Hughes TF, Friesner RA. Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450. Protein Science : a Publication of the Protein Society. PMID 26441133 DOI: 10.1002/Pro.2819 |
0.805 |
|
| 2015 |
Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, ... ... Friesner RA, et al. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/Ja512751Q |
0.773 |
|
| 2015 |
Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational preferences underlying reduced activity of a thermophilic ribonuclease H. Journal of Molecular Biology. 427: 853-66. PMID 25550198 DOI: 10.1016/J.Jmb.2014.11.023 |
0.557 |
|
| 2015 |
Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor. The Journal of Physical Chemistry. B. 119: 824-35. PMID 25395044 DOI: 10.1021/Jp5053612 |
0.802 |
|
| 2015 |
Mondal J, Friesner R, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Protein Biophysical Journal. 108: 12a. DOI: 10.1016/J.Bpj.2014.11.093 |
0.549 |
|
| 2014 |
Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. Journal of Chemical Theory and Computation. 10: 3207-20. PMID 26588291 DOI: 10.1021/Ct500189S |
0.552 |
|
| 2014 |
Mondal J, Friesner RA, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase. Journal of Chemical Theory and Computation. 10: 5696-5705. PMID 25516727 DOI: 10.1021/Ct500584N |
0.546 |
|
| 2014 |
Weisman AL, DuBay KH, Willets KA, Friesner RA. A first-principles polarized Raman method for determining whether a uniform region of a sample is crystalline or isotropic. The Journal of Chemical Physics. 141: 224702. PMID 25494765 DOI: 10.1063/1.4903308 |
0.725 |
|
| 2014 |
Jerome SV, Hughes TF, Friesner RA. Accurate pKa prediction in first-row hexaaqua transition metal complexes using the B3LYP-DBLOC method. The Journal of Physical Chemistry. B. 118: 8008-16. PMID 24707985 DOI: 10.1021/Jp501086H |
0.794 |
|
| 2014 |
Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins. 82: 1646-55. PMID 24619874 DOI: 10.1002/Prot.24551 |
0.348 |
|
| 2014 |
Zhang J, Steigerwald M, Brus L, Friesner RA. Covalent O-H bonds as electron traps in proton-rich rutile TiO2 nanoparticles. Nano Letters. 14: 1785-9. PMID 24611728 DOI: 10.1021/Nl404307N |
0.319 |
|
| 2014 |
Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging data fusion strategies in multireceptor lead optimization MM/GBSA end-point methods Journal of Chemical Theory and Computation. 10: 3207-3220. DOI: 10.1021/ct500189s |
0.441 |
|
| 2013 |
Robustelli P, Trbovic N, Friesner RA, Palmer AG. Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4. Journal of Chemical Theory and Computation. 9. PMID 24409105 DOI: 10.1021/Ct400654R |
0.358 |
|
| 2013 |
Miller EB, Murrett CS, Zhu K, Zhao S, Goldfeld DA, Bylund JH, Friesner RA. Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. Journal of Chemical Theory and Computation. 9: 1846-4864. PMID 23814507 DOI: 10.1021/Ct301083Q |
0.803 |
|
| 2013 |
Friesner RA, Abel R, Goldfeld DA, Miller EB, Murrett CS. Computational methods for high resolution prediction and refinement of protein structures. Current Opinion in Structural Biology. 23: 177-84. PMID 23688933 DOI: 10.1016/J.Sbi.2013.01.010 |
0.807 |
|
| 2013 |
Goldfeld DA, Friesner RA. The protein local optimization program and G-protein-coupled receptors: loop restoration and applications to homology modeling. Methods in Enzymology. 522: 1-20. PMID 23374177 DOI: 10.1016/B978-0-12-407865-9.00001-7 |
0.779 |
|
| 2013 |
Zeiske T, Stafford KA, Friesner RA, Palmer AG. Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins. 81: 499-509. PMID 23161667 DOI: 10.1002/Prot.24209 |
0.357 |
|
| 2013 |
Goldfeld DA, Zhu K, Beuming T, Friesner RA. Loop prediction for a GPCR homology model: algorithms and results. Proteins. 81: 214-28. PMID 22965891 DOI: 10.1002/Prot.24178 |
0.795 |
|
| 2013 |
Bochevarov AD, Harder E, Hughes TF, Greenwood JR, Braden DA, Philipp DM, Rinaldo D, Halls MD, Zhang J, Friesner RA. Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences International Journal of Quantum Chemistry. 113: 2110-2142. DOI: 10.1002/Qua.24481 |
0.369 |
|
| 2012 |
DuBay KH, Hall ML, Hughes TF, Wu C, Reichman DR, Friesner RA. Accurate Force Field Development for Modeling Conjugated Polymers. Journal of Chemical Theory and Computation. 8: 4556-4569. PMID 26605615 DOI: 10.1021/Ct300175W |
0.789 |
|
| 2012 |
Hughes TF, Friesner RA. Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450. Journal of Chemical Theory and Computation. 8: 442-59. PMID 26596595 DOI: 10.1021/Ct2006693 |
0.37 |
|
| 2012 |
Shivakumar D, Harder E, Damm W, Friesner RA, Sherman W. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field. Journal of Chemical Theory and Computation. 8: 2553-8. PMID 26592101 DOI: 10.1021/Ct300203W |
0.37 |
|
| 2012 |
Zhang J, Hughes TF, Steigerwald M, Brus L, Friesner RA. Realistic cluster modeling of electron transport and trapping in solvated TiO2 nanoparticles. Journal of the American Chemical Society. 134: 12028-42. PMID 22738308 DOI: 10.1021/Ja3013787 |
0.302 |
|
| 2012 |
Repasky MP, Murphy RB, Banks JL, Greenwood JR, Tubert-Brohman I, Bhat S, Friesner RA. Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide. Journal of Computer-Aided Molecular Design. 26: 787-99. PMID 22576241 DOI: 10.1007/S10822-012-9575-9 |
0.317 |
|
| 2012 |
Heckel JC, Weisman AL, Schneebeli ST, Hall ML, Sherry LJ, Stranahan SM, DuBay KH, Friesner RA, Willets KA. Polarized Raman spectroscopy of oligothiophene crystals to determine unit cell orientation. The Journal of Physical Chemistry. A. 116: 6804-16. PMID 22571336 DOI: 10.1021/Jp304192V |
0.774 |
|
| 2012 |
Hughes TF, Harvey JN, Friesner RA. A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation. Physical Chemistry Chemical Physics : Pccp. 14: 7724-38. PMID 22513477 DOI: 10.1039/C2Cp40220C |
0.364 |
|
| 2012 |
Wang L, Berne BJ, Friesner RA. On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proceedings of the National Academy of Sciences of the United States of America. 109: 1937-42. PMID 22308365 DOI: 10.1073/Pnas.1114017109 |
0.597 |
|
| 2012 |
Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 20 (8275-8280) 10.1073/pnas.1016951108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9665. DOI: 10.1073/pnas.1207511109 |
0.748 |
|
| 2012 |
Wang L, Berne BJ, Friesner RA. Ligand binding to protein-binding pockets with wet and dry regions (Proceedings of the National Academy of Sciences (2011) 108, 4 (1326-1330) DOI: 10.1073/pnas.1016793108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9220. DOI: 10.1073/pnas.1207504109 |
0.431 |
|
| 2012 |
Dubay KH, Hall ML, Hughes TF, Wu C, Reichman DR, Friesner RA. Accurate force field development for modeling conjugated polymers Journal of Chemical Theory and Computation. 8: 4556-4569. DOI: 10.1021/ct300175w |
0.765 |
|
| 2011 |
Hughes TF, Friesner RA. Correcting Systematic Errors in DFT Spin-Splitting Energetics for Transition Metal Complexes. Journal of Chemical Theory and Computation. 7: 19-32. PMID 26606215 DOI: 10.1021/Ct100359X |
0.377 |
|
| 2011 |
Li J, Schneebeli ST, Bylund J, Farid R, Friesner RA. IDSite: An accurate approach to predict P450-mediated drug metabolism. Journal of Chemical Theory and Computation. 7: 3829-3845. PMID 22247702 DOI: 10.1021/Ct200462Q |
0.779 |
|
| 2011 |
Schneebeli ST, Bochevarov AD, Friesner RA. Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies. Journal of Chemical Theory and Computation. 7: 658-668. PMID 22058661 DOI: 10.1021/Ct100651F |
0.668 |
|
| 2011 |
Zhao S, Zhu K, Li J, Friesner RA. Progress in super long loop prediction. Proteins. 79: 2920-35. PMID 21905115 DOI: 10.1002/Prot.23129 |
0.661 |
|
| 2011 |
Li J, Abel R, Zhu K, Cao Y, Zhao S, Friesner RA. The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 79: 2794-812. PMID 21905107 DOI: 10.1002/Prot.23106 |
0.743 |
|
| 2011 |
Wang L, Friesner RA, Berne BJ. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). The Journal of Physical Chemistry. B. 115: 9431-8. PMID 21714551 DOI: 10.1021/Jp204407D |
0.518 |
|
| 2011 |
Hughes TF, Friesner RA. Systematic investigation of the catalytic cycle of a single site ruthenium oxygen evolving complex using density functional theory. The Journal of Physical Chemistry. B. 115: 9280-9. PMID 21678966 DOI: 10.1021/Jp2026576 |
0.401 |
|
| 2011 |
Bounos G, Ghosh S, Lee AK, Plunkett KN, DuBay KH, Bolinger JC, Zhang R, Friesner RA, Nuckolls C, Reichman DR, Barbara PF. Controlling chain conformation in conjugated polymers using defect inclusion strategies. Journal of the American Chemical Society. 133: 10155-60. PMID 21612291 DOI: 10.1021/Ja2006687 |
0.758 |
|
| 2011 |
Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America. 108: 8275-80. PMID 21536915 DOI: 10.1073/Pnas.1016951108 |
0.796 |
|
| 2011 |
Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. Journal of the American Chemical Society. 133: 7384-97. PMID 21517016 DOI: 10.1021/Ja110287Y |
0.603 |
|
| 2011 |
Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. Chemmedchem. 6: 1049-66. PMID 21506273 DOI: 10.1002/Cmdc.201000533 |
0.573 |
|
| 2011 |
Schneebeli ST, Kamenetska M, Cheng Z, Skouta R, Friesner RA, Venkataraman L, Breslow R. Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections. Journal of the American Chemical Society. 133: 2136-9. PMID 21265533 DOI: 10.1021/Ja111320N |
0.7 |
|
| 2011 |
Wang L, Berne BJ, Friesner RA. Ligand binding to protein-binding pockets with wet and dry regions. Proceedings of the National Academy of Sciences of the United States of America. 108: 1326-30. PMID 21205906 DOI: 10.1073/Pnas.1016793108 |
0.554 |
|
| 2011 |
Goldfeld DA, Zhu K, Beuming T, Friesner RA. Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein-coupled receptors Proceedings of the National Academy of Sciences of the United States of America. 108: E342. DOI: 10.1073/Pnas.1108089108 |
0.787 |
|
| 2010 |
Hall ML, Zhang J, Bochevarov AD, Friesner RA. Continuous Localized Orbital Corrections to Density Functional Theory: B3LYP-CLOC. Journal of Chemical Theory and Computation. 6: 3647-3663. PMID 21286233 DOI: 10.1021/Ct100418N |
0.557 |
|
| 2010 |
Bochevarov AD, Friesner RA, Lippard SJ. The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study. Journal of Chemical Theory and Computation. 6: 3735-3749. PMID 21258606 DOI: 10.1021/Ct100398M |
0.47 |
|
| 2010 |
Abel R, Wang L, Friesner RA, Berne BJ. A displaced-solvent functional analysis of model hydrophobic enclosures. Journal of Chemical Theory and Computation. 6: 2924-2934. PMID 21135914 DOI: 10.1021/Ct100215C |
0.696 |
|
| 2010 |
Wang L, Friesner RA, Berne BJ. Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models. Faraday Discussions. 146: 247-62; discussion 2. PMID 21043426 DOI: 10.1039/B925521B |
0.551 |
|
| 2010 |
Wang L, Friesner RA, Berne BJ. Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures. The Journal of Physical Chemistry. B. 114: 7294-301. PMID 20443643 DOI: 10.1021/Jp100772W |
0.528 |
|
| 2010 |
Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC. ConfGen: a conformational search method for efficient generation of bioactive conformers. Journal of Chemical Information and Modeling. 50: 534-46. PMID 20373803 DOI: 10.1021/Ci100015J |
0.372 |
|
| 2010 |
Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ. Dewetting transitions in protein cavities. Proteins. 78: 1856-69. PMID 20225258 DOI: 10.1002/Prot.22699 |
0.653 |
|
| 2010 |
Friesner R, Wertheimer R. Model for primary charge separation in reaction centers of photosynthetic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 79: 2138-42. PMID 16593176 DOI: 10.1073/Pnas.79.6.2138 |
0.313 |
|
| 2009 |
Hall ML, Goldfeld DA, Bochevarov AD, Friesner RA. Localized orbital corrections for the calculation of barrier heights in density functional theory. Journal of Chemical Theory and Computation. 5: 2996-3009. PMID 20161583 DOI: 10.1021/Ct9003965 |
0.81 |
|
| 2009 |
Tian L, Friesner RA. QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. Journal of Chemical Theory and Computation. 5: 1421-1431. PMID 20046929 DOI: 10.1021/Ct900040N |
0.503 |
|
| 2009 |
Wang L, Abel R, Friesner RA, Berne BJ. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. Journal of Chemical Theory and Computation. 5: 1462-1473. PMID 19851475 DOI: 10.1021/Ct900078K |
0.638 |
|
| 2009 |
Schneebeli ST, Hall ML, Breslow R, Friesner R. Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations. Journal of the American Chemical Society. 131: 3965-73. PMID 19243187 DOI: 10.1021/Ja806951R |
0.771 |
|
| 2009 |
Trbovic N, Cho JH, Abel R, Friesner RA, Rance M, Palmer AG. Protein side-chain dynamics and residual conformational entropy. Journal of the American Chemical Society. 131: 615-22. PMID 19105660 DOI: 10.1021/Ja806475K |
0.549 |
|
| 2009 |
Blagojevic V, Chen YR, Steigerwald M, Brus L, Friesner RA. Quantum chemical investigation of cluster models for TiO 2 nanoparticles with water-derived ligand passivation: Studies of excess electron states and implications for charge transport in the Gratzel cell Journal of Physical Chemistry C. 113: 19806-19811. DOI: 10.1021/Jp905332Z |
0.33 |
|
| 2009 |
Wang T, Friesner RA. Computational modeling of the electronic structure of Oligothiophenes with various side chains Journal of Physical Chemistry C. 113: 2553-2561. DOI: 10.1021/Jp807733E |
0.334 |
|
| 2008 |
Goldfeld DA, Bochevarov AD, Friesner RA. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions. The Journal of Chemical Physics. 129: 214105. PMID 19063542 DOI: 10.1063/1.3008062 |
0.776 |
|
| 2008 |
Rinaldo D, Tian L, Harvey JN, Friesner RA. Density functional localized orbital corrections for transition metals. The Journal of Chemical Physics. 129: 164108. PMID 19045248 DOI: 10.1063/1.2974101 |
0.525 |
|
| 2008 |
Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Journal of Chemical Theory and Computation. 4: 855-868. PMID 18787648 DOI: 10.1021/Ct800051K |
0.412 |
|
| 2008 |
Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallographica. Section D, Biological Crystallography. 64: 383-96. PMID 18391405 DOI: 10.1107/S090744490800070X |
0.36 |
|
| 2008 |
Ko C, Malick DK, Braden DA, Friesner RA, Martínez TJ. Pseudospectral time-dependent density functional theory. The Journal of Chemical Physics. 128: 104103. PMID 18345873 DOI: 10.1063/1.2834222 |
0.365 |
|
| 2008 |
Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/Jp077018H |
0.339 |
|
| 2008 |
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 72: 959-71. PMID 18300241 DOI: 10.1002/Prot.21990 |
0.678 |
|
| 2008 |
Abel R, Young T, Farid R, Berne BJ, Friesner RA. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. Journal of the American Chemical Society. 130: 2817-31. PMID 18266362 DOI: 10.1021/Ja0771033 |
0.672 |
|
| 2008 |
Bochevarov AD, Friesner RA. The densities produced by the density functional theory: comparison to full configuration interaction. The Journal of Chemical Physics. 128: 034102. PMID 18205483 DOI: 10.1063/1.2821123 |
0.317 |
|
| 2008 |
Trbovic N, Kim B, Friesner RA, Palmer AG. Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation. Proteins. 71: 684-94. PMID 17975832 DOI: 10.1002/Prot.21750 |
0.542 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 3: 640-8. PMID 26637042 DOI: 10.1021/Ct600129F |
0.679 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA. 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. Journal of Chemical Theory and Computation. 3: 2108-19. PMID 26636204 DOI: 10.1021/Ct700166F |
0.65 |
|
| 2007 |
Repasky MP, Shelley M, Friesner RA. Flexible ligand docking with Glide. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.12. PMID 18428795 DOI: 10.1002/0471250953.Bi0812S18 |
0.325 |
|
| 2007 |
Zhou Z, Felts AK, Friesner RA, Levy RM. Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. Journal of Chemical Information and Modeling. 47: 1599-608. PMID 17585856 DOI: 10.1021/Ci7000346 |
0.324 |
|
| 2007 |
Huang X, Hagen M, Kim B, Friesner RA, Zhou R, Berne BJ. Replica exchange with solute tempering: efficiency in large scale systems. The Journal of Physical Chemistry. B. 111: 5405-10. PMID 17439169 DOI: 10.1021/Jp068826W |
0.707 |
|
| 2007 |
Rinaldo D, Philipp DM, Lippard SJ, Friesner RA. Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. Journal of the American Chemical Society. 129: 3135-47. PMID 17326634 DOI: 10.1021/Ja0654074 |
0.522 |
|
| 2007 |
Hagen M, Kim B, Liu P, Friesner RA, Berne BJ. Serial replica exchange. The Journal of Physical Chemistry. B. 111: 1416-23. PMID 17249714 DOI: 10.1021/Jp064479E |
0.651 |
|
| 2007 |
Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 66: 814-23. PMID 17206724 DOI: 10.1002/Prot.21099 |
0.671 |
|
| 2007 |
Young T, Abel R, Kim B, Berne BJ, Friesner RA. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proceedings of the National Academy of Sciences of the United States of America. 104: 808-13. PMID 17204562 DOI: 10.1073/Pnas.0610202104 |
0.729 |
|
| 2007 |
Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 66: 824-37. PMID 17154422 DOI: 10.1002/Prot.21125 |
0.672 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA. 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 Journal of Chemical Theory and Computation. 3: 2108-2119. DOI: 10.1021/ct700166f |
0.567 |
|
| 2007 |
Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f |
0.672 |
|
| 2006 |
Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design. 20: 647-71. PMID 17124629 DOI: 10.1007/S10822-006-9087-6 |
0.56 |
|
| 2006 |
Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry. 49: 6177-96. PMID 17034125 DOI: 10.1021/Jm051256O |
0.38 |
|
| 2006 |
Friesner RA, Knoll EH, Cao Y. A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction scheme. The Journal of Chemical Physics. 125: 124107. PMID 17014166 DOI: 10.1063/1.2263795 |
0.643 |
|
| 2006 |
Knoll EH, Friesner RA. Localized orbital corrections for the calculation of ionization potentials and electron affinities in density functional theory. The Journal of Physical Chemistry. B. 110: 18787-802. PMID 16986869 DOI: 10.1021/Jp0619888 |
0.644 |
|
| 2006 |
Zhu K, Pincus DL, Zhao S, Friesner RA. Long loop prediction using the protein local optimization program. Proteins. 65: 438-52. PMID 16927380 DOI: 10.1002/Prot.21040 |
0.733 |
|
| 2006 |
Ravindranathan KP, Gallicchio E, Friesner RA, McDermott AE, Levy RM. Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. Journal of the American Chemical Society. 128: 5786-91. PMID 16637647 DOI: 10.1021/Ja058465I |
0.584 |
|
| 2006 |
Guallar V, Jarzecki AA, Friesner RA, Spiro TG. Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. Journal of the American Chemical Society. 128: 5427-35. PMID 16620114 DOI: 10.1021/Ja057318H |
0.358 |
|
| 2006 |
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry. 49: 534-53. PMID 16420040 DOI: 10.1021/Jm050540C |
0.567 |
|
| 2006 |
Farid R, Day T, Friesner RA, Pearlstein RA. New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorganic & Medicinal Chemistry. 14: 3160-73. PMID 16413785 DOI: 10.1016/J.Bmc.2005.12.032 |
0.337 |
|
| 2006 |
Yu Z, Jacobson MP, Friesner RA. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Journal of Computational Chemistry. 27: 72-89. PMID 16261581 DOI: 10.1002/Jcc.20307 |
0.632 |
|
| 2006 |
Friesner RA, Jordan KD, Reichman D. Tribute to Robert J. Silbey The Journal of Physical Chemistry B. 110: 18734-18734. DOI: 10.1021/Jp062035C |
0.579 |
|
| 2005 |
Maple JR, Cao Y, Damm W, Halgren TA, Kaminski GA, Zhang LY, Friesner RA. A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions. Journal of Chemical Theory and Computation. 1: 694-715. PMID 26641692 DOI: 10.1021/Ct049855I |
0.422 |
|
| 2005 |
Kaminski GA, Maple JR, Murphy RB, Braden DA, Friesner RA. Pseudospectral Local Second-Order Møller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs. Journal of Chemical Theory and Computation. 1: 248-54. PMID 26641295 DOI: 10.1021/Ct049880O |
0.409 |
|
| 2005 |
Harder E, Kim B, Friesner RA, Berne BJ. Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water. Journal of Chemical Theory and Computation. 1: 169-80. PMID 26641127 DOI: 10.1021/Ct049914S |
0.657 |
|
| 2005 |
Kim B, Young T, Harder E, Friesner RA, Berne BJ. 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. The Journal of Physical Chemistry. B. 109: 16529-38. PMID 16853101 DOI: 10.1021/Jp051569V |
0.624 |
|
| 2005 |
Friesner RA. Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results. Advances in Protein Chemistry. 72: 79-104. PMID 16581373 DOI: 10.1016/S0065-3233(05)72003-9 |
0.409 |
|
| 2005 |
Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, ... Friesner RA, et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry. 26: 1752-80. PMID 16211539 DOI: 10.1002/Jcc.20292 |
0.538 |
|
| 2005 |
Jovanovic T, Farid R, Friesner RA, McDermott AE. Thermal equilibrium of high- and low-spin forms of cytochrome P450 BM-3: repositioning of the substrate? Journal of the American Chemical Society. 127: 13548-52. PMID 16190718 DOI: 10.1021/Ja0524604 |
0.588 |
|
| 2005 |
Liu P, Kim B, Friesner RA, Berne BJ. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proceedings of the National Academy of Sciences of the United States of America. 102: 13749-54. PMID 16172406 DOI: 10.1073/Pnas.0506346102 |
0.631 |
|
| 2005 |
Chakrabarti R, Klibanov AM, Friesner RA. Sequence optimization and designability of enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. 102: 12035-40. PMID 16103370 DOI: 10.1073/Pnas.0505397102 |
0.329 |
|
| 2005 |
Chakrabarti R, Klibanov AM, Friesner RA. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proceedings of the National Academy of Sciences of the United States of America. 102: 10153-8. PMID 15998733 DOI: 10.1073/Pnas.0504023102 |
0.36 |
|
| 2005 |
Cao Y, Beachy MD, Braden DA, Morrill L, Ringnalda MN, Friesner RA. Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods. The Journal of Chemical Physics. 122: 224116. PMID 15974660 DOI: 10.1063/1.1924598 |
0.355 |
|
| 2005 |
Friesner RA. Ab initio quantum chemistry: methodology and applications. Proceedings of the National Academy of Sciences of the United States of America. 102: 6648-53. PMID 15870212 DOI: 10.1073/Pnas.0408036102 |
0.347 |
|
| 2005 |
Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of Computational Chemistry. 26: 915-31. PMID 15841474 DOI: 10.1002/Jcc.20222 |
0.56 |
|
| 2005 |
Cao Y, Friesner RA. Molecular (hyper)polarizabilities computed by pseudospectral methods. The Journal of Chemical Physics. 122: 104102. PMID 15836304 DOI: 10.1063/1.1855881 |
0.353 |
|
| 2005 |
Friesner RA, Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annual Review of Physical Chemistry. 56: 389-427. PMID 15796706 DOI: 10.1146/Annurev.Physchem.55.091602.094410 |
0.349 |
|
| 2005 |
Gherman BF, Lippard SJ, Friesner RA. Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques. Journal of the American Chemical Society. 127: 1025-37. PMID 15656641 DOI: 10.1021/Ja049847B |
0.773 |
|
| 2005 |
Zhou Z, Steigerwald ML, Friesner RA, Brus L, Hybertsen MS. Structural and chemical trends in doped silicon nanocrystals: First-principles calculations Physical Review B - Condensed Matter and Materials Physics. 71. DOI: 10.1103/Physrevb.71.245308 |
0.39 |
|
| 2005 |
Zhou Z, Steigerwald ML, Friesner RA, Brus L, Hybertsen MS. Dopant local bonding and electrical activity near Si(001)-oxide interfaces Journal of Applied Physics. 98. DOI: 10.1063/1.2071447 |
0.31 |
|
| 2005 |
Harder E, Kim B, Friesner RA, Berne BJ. Efficient simulation method for polarizable protein force fields: Application to the simulation of BPTI in liquid water Journal of Chemical Theory and Computation. 1: 169-180. DOI: 10.1021/ct049914s |
0.568 |
|
| 2004 |
Friesner RA. Combined quantum and molecular mechanics (QM/MM). Drug Discovery Today. Technologies. 1: 253-60. PMID 24981493 DOI: 10.1016/J.Ddtec.2004.11.008 |
0.31 |
|
| 2004 |
Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophysical Journal. 87: 3448-59. PMID 15339802 DOI: 10.1529/Biophysj.104.046417 |
0.56 |
|
| 2004 |
Guallar V, Friesner RA. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. Journal of the American Chemical Society. 126: 8501-8. PMID 15238007 DOI: 10.1021/Ja036123B |
0.36 |
|
| 2004 |
Gherman BF, Goldberg SD, Cornish VW, Friesner RA. 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. Journal of the American Chemical Society. 126: 7652-64. PMID 15198613 DOI: 10.1021/Ja036879A |
0.719 |
|
| 2004 |
Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 55: 368-82. PMID 15048828 DOI: 10.1002/Prot.20014 |
0.613 |
|
| 2004 |
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 55: 351-67. PMID 15048827 DOI: 10.1002/Prot.10613 |
0.795 |
|
| 2004 |
Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry. 47: 1750-9. PMID 15027866 DOI: 10.1021/Jm030644S |
0.328 |
|
| 2004 |
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry. 47: 1739-49. PMID 15027865 DOI: 10.1021/Jm0306430 |
0.646 |
|
| 2004 |
Zhou Z, Steigerwald M, Hybertsen M, Brus L, Friesner RA. Electronic structure of tubular aromatic molecules derived from the metallic (5,5) armchair single wall carbon nanotube. Journal of the American Chemical Society. 126: 3597-607. PMID 15025489 DOI: 10.1021/Ja039294P |
0.35 |
|
| 2004 |
Guallar V, Jacobson M, McDermott A, Friesner RA. Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of Molecular Biology. 337: 227-39. PMID 15001364 DOI: 10.1016/J.Jmb.2003.11.016 |
0.708 |
|
| 2004 |
Gherman BF, Baik MH, Lippard SJ, Friesner RA. Dioxygen activation in methane monooxygenase: a theoretical study. Journal of the American Chemical Society. 126: 2978-90. PMID 14995216 DOI: 10.1021/Ja036506+ |
0.785 |
|
| 2004 |
Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: Correction of systematic errors in implicit solvent models Journal of Physical Chemistry B. 108: 6643-6654. DOI: 10.1021/Jp037821L |
0.675 |
|
| 2004 |
Rim KT, Müller T, Fitts JP, Adib K, Camillone N, Osgood RM, Batista ER, Friesner RA, Joyce SA, Flynn GW. Scanning tunneling microscopy and theoretical study of competitive reactions in the dissociative chemisorption of CCl 4 on iron oxide surfaces Journal of Physical Chemistry B. 108: 16753-16760. DOI: 10.1021/Jp030937X |
0.535 |
|
| 2004 |
Kaminski GA, Stern HA, Berne BJ, Friesner RA. Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry Journal of Physical Chemistry A. 108: 621-627. DOI: 10.1021/Jp0301103 |
0.556 |
|
| 2004 |
Baik MH, Friesner RA, Parkin G. Theoretical investigation of the metal-metal interaction in dimolybdenum complexes with bridging hydride and methyl ligands Polyhedron. 23: 2879-2900. DOI: 10.1016/J.Poly.2004.08.004 |
0.534 |
|
| 2003 |
Baik MH, Friesner RA, Lippard SJ. cis-[Pt(NH3)2(L)]2+/+ (L = Cl, H2O, NH3) binding to purines and CO: does pi-back-donation play a role? Inorganic Chemistry. 42: 8615-7. PMID 14686835 DOI: 10.1021/Ic035022B |
0.56 |
|
| 2003 |
Zhou Z, Friesner RA, Brus L. Electronic structure of 1 to 2 nm diameter silicon core/shell nanocrystals: surface chemistry, optical spectra, charge transfer, and doping. Journal of the American Chemical Society. 125: 15599-607. PMID 14664607 DOI: 10.1021/Ja036443V |
0.318 |
|
| 2003 |
Baik MH, Friesner RA, Lippard SJ. Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? Journal of the American Chemical Society. 125: 14082-92. PMID 14611245 DOI: 10.1021/Ja036960D |
0.595 |
|
| 2003 |
Tang L, Papish ET, Abramo GP, Norton JR, Baik MH, Friesner RA, Rappé A. Kinetics and thermodynamics of H. transfer from (eta5-C5R5)Cr(CO)3H (R = Ph, Me, H) to methyl methacrylate and styrene. Journal of the American Chemical Society. 125: 10093-102. PMID 12914473 DOI: 10.1021/Ja034927L |
0.49 |
|
| 2003 |
Baik MH, Newcomb M, Friesner RA, Lippard SJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chemical Reviews. 103: 2385-419. PMID 12797835 DOI: 10.1021/Cr950244F |
0.553 |
|
| 2003 |
Guallar V, Baik MH, Lippard SJ, Friesner RA. Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450. Proceedings of the National Academy of Sciences of the United States of America. 100: 6998-7002. PMID 12771375 DOI: 10.1073/Pnas.0732000100 |
0.624 |
|
| 2003 |
Wirstam M, Lippard SJ, Friesner RA. Reversible dioxygen binding to hemerythrin. Journal of the American Chemical Society. 125: 3980-7. PMID 12656634 DOI: 10.1021/Ja017692R |
0.519 |
|
| 2003 |
Kaminski GA, Friesner RA, Zhou R. A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. Journal of Computational Chemistry. 24: 267-76. PMID 12548718 DOI: 10.1002/Jcc.10170 |
0.58 |
|
| 2003 |
Friesner RA, Baik MH, Gherman BF, Guallar V, Wirstam M, Murphy RB, Lippard SJ. How iron-containing proteins control dioxygen chemistry: A detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations Coordination Chemistry Reviews. 238: 267-290. DOI: 10.1016/S0010-8545(02)00284-9 |
0.809 |
|
| 2002 |
Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054 |
0.603 |
|
| 2002 |
Hascall T, Baik MH, Bridgewater BM, Shin JH, Churchill DG, Friesner RA, Parkin G. A non-classical hydrogen bond in the molybdenum arene complex [eta 6-C6H5C6H3(Ph)OH]Mo(PMe3)3: evidence that hydrogen bonding facilitates oxidative addition of the O-H bond. Chemical Communications (Cambridge, England). 2644-5. PMID 12510278 DOI: 10.1039/B208678F |
0.493 |
|
| 2002 |
Baik MH, Gherman BF, Friesner RA, Lippard SJ. Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q. Journal of the American Chemical Society. 124: 14608-15. PMID 12465971 DOI: 10.1021/Ja026794U |
0.785 |
|
| 2002 |
Baik MH, Crystal JB, Friesner RA. Ab initio quantum calculation of the diabatic coupling matrix elements for the self-exchange redox couples M(Cp)20/+ (M = Fe, Co; Cp = C5H5). Inorganic Chemistry. 41: 5926-7. PMID 12425612 DOI: 10.1021/Ic025895Q |
0.518 |
|
| 2002 |
Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. Journal of Computational Chemistry. 23: 1515-31. PMID 12395421 DOI: 10.1002/Jcc.10125 |
0.681 |
|
| 2002 |
Ambundo EA, Friesner RA, Lippard SJ. Reactions of methane monooxygenase intermediate Q with derivatized methanes. Journal of the American Chemical Society. 124: 8770-1. PMID 12137510 DOI: 10.1021/Ja0265759 |
0.394 |
|
| 2002 |
An Y, Friesner RA. A novel fold recognition method using composite predicted secondary structures. Proteins. 48: 352-66. PMID 12112702 DOI: 10.1002/Prot.10145 |
0.527 |
|
| 2002 |
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology. 320: 597-608. PMID 12096912 DOI: 10.1016/S0022-2836(02)00470-9 |
0.654 |
|
| 2002 |
Guallar V, Gherman BF, Lippard SJ, Friesner RA. Quantum chemical studies of methane monooxygenase: comparision with P450. Current Opinion in Chemical Biology. 6: 236-42. PMID 12039010 DOI: 10.1016/S1367-5931(02)00310-1 |
0.762 |
|
| 2002 |
Baik MH, Friesner RA, Lippard SJ. Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? Journal of the American Chemical Society. 124: 4495-503. PMID 11960480 DOI: 10.1021/Ja017588+ |
0.606 |
|
| 2002 |
Guallar V, Gherman BF, Miller WH, Lippard SJ, Friesner RA. Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase. Journal of the American Chemical Society. 124: 3377-84. PMID 11916423 DOI: 10.1021/Ja0167248 |
0.742 |
|
| 2002 |
Baik MH, Friesner RA. Computing redox potentials in solution: Density functional theory as a tool for rational design of redox agents Journal of Physical Chemistry A. 106: 7407-7412. DOI: 10.1021/Jp025853N |
0.562 |
|
| 2002 |
Jacobson MP, Kaminski GA, Friesner RA, Rapp CS. Force field validation using protein side chain prediction Journal of Physical Chemistry B. 106: 11673-11680. DOI: 10.1021/Jp021564N |
0.61 |
|
| 2002 |
Margulis CJ, Guallar V, Sim E, Friesner RA, Berne BJ. A new semiempirical approach to study ground and excited states of metal complexes in biological systems Journal of Physical Chemistry B. 106: 8038-8046. DOI: 10.1021/Jp020705I |
0.565 |
|
| 2002 |
Batista ER, Friesner RA. A self-consistent charge-embedding methodology for ab initio quantum chemical cluster modeling of ionic solids and surfaces: Application to the (001) surface of hematite (α-Fe2O3) Journal of Physical Chemistry B. 106: 8136-8141. DOI: 10.1021/Jp020509B |
0.566 |
|
| 2002 |
Crystal J, Zhang LY, Friesner RA, Flynn GW. Computational modeling for scanning tunneling microscopy of physisorbed molecules via ab initio quantum chemistry Journal of Physical Chemistry A. 106: 1802-1814. DOI: 10.1021/Jp012629+ |
0.324 |
|
| 2002 |
Klicić JJ, Friesner RA, Liu SY, Guida WC. Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods Journal of Physical Chemistry A. 106: 1327-1335. DOI: 10.1021/Jp012533F |
0.403 |
|
| 2002 |
Eyrich VA, Friesner RA, Standley DM. AB initio protein structure prediction using a size-dependent tertiary folding potential Advances in Chemical Physics. 120: 223-263. |
0.781 |
|
| 2002 |
Hascall T, Baik MH, Bridgewater BM, Shin JH, Churchill DG, Friesner RA, Parkin G. A non-classical hydrogen bond in the molybdenum arene complex [η6-C6H5C6H3(Ph) OH]Mo(PMe3)3: Evidence that hydrogen bonding facilitates oxidative addition of the O-H bond Chemical Communications. 2644-2645. |
0.42 |
|
| 2001 |
Standley DM, Eyrich VA, An Y, Pincus DL, Gunn JR, Friesner RA. Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins. 133-9. PMID 11835490 DOI: 10.1002/Prot.10005 |
0.804 |
|
| 2001 |
Shin JH, Bridgewater BM, Churchill DG, Baik MH, Friesner RA, Parkin G. An experimental and computational analysis of the formation of the terminal nitrido complex (eta3-Cp*)2Mo(N)(N3) by elimination of N2 from Cp*2Mo(N3)2: the barrier to elimination is strongly influenced by the exo versus endo configuration of the azide ligand. Journal of the American Chemical Society. 123: 10111-2. PMID 11592896 DOI: 10.1021/Ja011416V |
0.484 |
|
| 2001 |
Gherman BF, Dunietz BD, Whittington DA, Lippard SJ, Friesner RA. Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. Journal of the American Chemical Society. 123: 3836-7. PMID 11457123 DOI: 10.1021/Ja0055108 |
0.768 |
|
| 2001 |
Friesner RA, Dunietz BD. Large-scale ab initio quantum chemical calculations on biological systems. Accounts of Chemical Research. 34: 351-8. PMID 11352713 DOI: 10.1021/Ar980111R |
0.659 |
|
| 2001 |
Baik M, Lee D, Friesner RA, Lippard SJ. Theoretical studies of diiron(II) complexes that model features of the dioxygen-activating centers in non-heme diiron enzymes Israel Journal of Chemistry. 41: 173-186. DOI: 10.1560/8Yug-V7Ef-Vhhp-6Ug2 |
0.618 |
|
| 2001 |
Dunietz BD, Friesner RA. Application and development of multiconfigurational localized perturbation theory Journal of Chemical Physics. 115: 11052-11067. DOI: 10.1063/1.1418442 |
0.641 |
|
| 2001 |
Stern HA, Rittner F, Berne BJ, Friesner RA. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function Journal of Chemical Physics. 115: 2237-2251. DOI: 10.1063/1.1376165 |
0.555 |
|
| 2001 |
Gherman BF, Friesner RA, Wong TH, Min Z, Bersohn R. Photodissociation of acetaldehyde: The CH4+CO channel Journal of Chemical Physics. 114: 6128-6133. DOI: 10.1063/1.1355983 |
0.727 |
|
| 2001 |
Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z |
0.557 |
|
| 2001 |
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides Journal of Physical Chemistry B. 105: 6474-6487. DOI: 10.1021/Jp003919D |
0.528 |
|
| 2001 |
Vargas R, Garza J, Friesner RA, Stern H, Hay BP, Dixon DA. Strength of the N-H⋯O=C and C-H⋯O=C bonds in formamide and N-methylacetamide dimers Journal of Physical Chemistry A. 105: 4963-4968. DOI: 10.1021/Jp003888M |
0.367 |
|
| 2001 |
Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations Journal of Computational Chemistry. 22: 591-607. DOI: 10.1002/Jcc.1031 |
0.389 |
|
| 2000 |
Murphy RB, Cao Y, Beachy MD, Ringnalda MN, Friesner RA. Efficient pseudospectral methods for density functional calculations Journal of Chemical Physics. 112: 10131-10141. DOI: 10.1063/1.481704 |
0.35 |
|
| 2000 |
Golosov AA, Friesner RA, Pechukas P. Reduced dynamics in spin-boson models: A method for both slow and fast bath Journal of Chemical Physics. 112: 2095-2105. DOI: 10.1063/1.480888 |
0.303 |
|
| 2000 |
Bridgewater BM, Fillebeen T, Friesner RA, Parkin G. A zinc thiolate species which mimics aspects of the chemistry of the Ada repair protein and matrix metalloproteinases: the synthesis, structure and reactivity of the tris(2-mercapto-1-phenylimidazolyl)hydroborato complex [TmPh]ZnSPh Journal of the Chemical Society-Dalton Transactions. 4494-4496. DOI: 10.1039/B007886G |
0.3 |
|
| 2000 |
Crystal J, Friesner RA. Calculation of the lonization potentials and electron affinities of bacteriochlorophyll and bacteriopheophytin via ab initio quantum chemistry Journal of Physical Chemistry A. 104: 2362-2366. DOI: 10.1021/Jp991318K |
0.407 |
|
| 2000 |
Dunietz BD, Beachy MD, Cao Y, Whittington DA, Lippard SJ, Friesner RA. Large scale ab initio quantum chemical calculation of the intermediates in the soluble methane monooxygenase catalytic cycle Journal of the American Chemical Society. 122: 2828-2839. DOI: 10.1021/Ja9920967 |
0.645 |
|
| 2000 |
Murphy RB, Philipp DM, Friesner RA. Frozen orbital QM/MM methods for density functional theory Chemical Physics Letters. 321: 113-120. DOI: 10.1016/S0009-2614(00)00289-X |
0.405 |
|
| 2000 |
Murphy RB, Philipp DM, Friesner RA. A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-Scale Modeling of Chemistry in Protein Environments Journal of Computational Chemistry. 21: 1442-1457. DOI: 10.1002/1096-987X(200012)21:16<1442::Aid-Jcc3>3.0.Co;2-O |
0.359 |
|
| 1999 |
Eyrich VA, Standley DM, Friesner RA. Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. Journal of Molecular Biology. 288: 725-42. PMID 10329175 DOI: 10.1006/Jmbi.1999.2702 |
0.804 |
|
| 1999 |
Rapp CS, Friesner RA. Prediction of loop geometries using a generalized born model of solvation effects. Proteins. 35: 173-83. PMID 10223290 DOI: 10.1002/(Sici)1097-0134(19990501)35:2<173::Aid-Prot4>3.0.Co;2-2 |
0.412 |
|
| 1999 |
Eyrich VA, Standley DM, Felts AK, Friesner RA. Protein tertiary structure prediction using a branch and bound algorithm. Proteins. 35: 41-57. PMID 10090285 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<41::Aid-Prot5>3.0.Co;2-N |
0.802 |
|
| 1999 |
Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE. A branch and bound algorithm for protein structure refinement from sparse NMR data sets Journal of Molecular Biology. 285: 1691-1710. PMID 9917406 DOI: 10.1006/Jmbi.1998.2372 |
0.815 |
|
| 1999 |
Banks JL, Kaminski GA, Zhou R, Mainz DT, Berne BJ, Friesner RA. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model The Journal of Chemical Physics. 110: 741-754. DOI: 10.1063/1.478043 |
0.646 |
|
| 1999 |
Dunietz BD, Murphy RB, Friesner RA. Calculation of atomization energies by a multiconfigurational localized perturbation theory - Application for closed shell cases Journal of Chemical Physics. 110: 1921-1930. DOI: 10.1063/1.477859 |
0.662 |
|
| 1999 |
Dunietz BD, Murphy RB, Friesner RA. Calculation of atomization energies by a multiconfigurational localized perturbation theory—Application for closed shell cases The Journal of Chemical Physics. 110: 1921-1930. DOI: 10.1063/1.477859 |
0.582 |
|
| 1999 |
Stern HA, Kaminski GA, Banks JL, Zhou R, Berne BJ, Friesner RA. Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry Journal of Physical Chemistry B. 103: 4730-4737. DOI: 10.1021/Jp984498R |
0.66 |
|
| 1999 |
Klicić JJ, Friesner RA. 1,3-Dipolar Addition of Phenylazide to the Carbon-Carbon Double Bond: An ab Initio Study Journal of Physical Chemistry A. 103: 1276-1282. DOI: 10.1021/Jp9839403 |
0.409 |
|
| 1999 |
Friesner RA. Correlated ab initio electronic structure calculations for large molecules Journal of Physical Chemistry A. 103: XI-1928. DOI: 10.1021/Jp9825157 |
0.394 |
|
| 1999 |
Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson-boltzmann analytical gradients for molecular modeling calculations Journal of Physical Chemistry B. 103: 3057-3061. DOI: 10.1021/Jp982513M |
0.36 |
|
| 1999 |
Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations The Journal of Physical Chemistry B. 103: 3057-3061. DOI: 10.1021/jp982513m |
0.474 |
|
| 1999 |
Philipp DM, Friesner RA. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide Journal of Computational Chemistry. 20: 1468-1494. DOI: 10.1002/(Sici)1096-987X(19991115)20:14<1468::Aid-Jcc2>3.0.Co;2-0 |
0.39 |
|
| 1998 |
Zhang LY, Friesner RA. Ab initio calculation of electronic coupling in the photosynthetic reaction center. Proceedings of the National Academy of Sciences of the United States of America. 95: 13603-5. PMID 9811846 DOI: 10.1073/Pnas.95.23.13603 |
0.328 |
|
| 1998 |
Standley DM, Gunn JR, Friesner RA, McDermott AE. Tertiary structure prediction of mixed α/β proteins via energy minimization Proteins: Structure, Function and Genetics. 33: 240-252. PMID 9779791 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<240::Aid-Prot8>3.0.Co;2-M |
0.606 |
|
| 1998 |
Friesner RA, Beachy MD. Quantum mechanical calculations on biological systems. Current Opinion in Structural Biology. 8: 257-62. PMID 9631302 DOI: 10.1016/S0959-440X(98)80048-1 |
0.339 |
|
| 1998 |
Liu YP, Kim K, Berne BJ, Friesner RA, Rick SW. Constructing ab initio force fields for molecular dynamics simulations Journal of Chemical Physics. 108: 4739-4755. DOI: 10.1063/1.475886 |
0.552 |
|
| 1998 |
Murphy RB, Friesner RA. Accurate quantum chemical calculation of the relative energetics of C20 carbon clusters via localized multireference perturbation calculations Chemical Physics Letters. 288: 403-407. DOI: 10.1016/S0009-2614(98)00324-8 |
0.351 |
|
| 1998 |
Chasman D, Beachy MD, Wang L, Friesner RA. Parallel pseudospectral electronic structure: I. Hartree-Fock calculations Journal of Computational Chemistry. 19: 1017-1029. DOI: 10.1002/(Sici)1096-987X(19980715)19:9<1017::Aid-Jcc3>3.0.Co;2-T |
0.319 |
|
| 1997 |
Zhang LY, Friesner RA, Murphy RB. Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules Journal of Chemical Physics. 107: 450-459. DOI: 10.1063/1.474406 |
0.379 |
|
| 1997 |
Cortis CM, Rossky PJ, Friesner RA. A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids Journal of Chemical Physics. 107: 6400-6414. DOI: 10.1063/1.474300 |
0.306 |
|
| 1997 |
Murphy RB, Pollard WT, Friesner RA. Pseudospectral localized generalized Mo/ller–Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies The Journal of Chemical Physics. 106: 5073-5084. DOI: 10.1063/1.473553 |
0.42 |
|
| 1997 |
Edinger SR, Cortis C, Shenkin PS, Friesner RA. Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation The Journal of Physical Chemistry B. 101: 1190-1197. DOI: 10.1021/Jp962156K |
0.34 |
|
| 1997 |
Kim K, Friesner RA. Hydrogen bonding between amino acid backbone and side chain analogues: A high-level ab initio study Journal of the American Chemical Society. 119: 12952-12961. DOI: 10.1021/Ja971836D |
0.316 |
|
| 1997 |
Beachy MD, Chasman D, Murphy RB, Halgren TA, Friesner RA. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields Journal of the American Chemical Society. 119: 5908-5920. DOI: 10.1021/Ja962310G |
0.408 |
|
| 1997 |
Black S, Friesner R, Lu P, Osgood R. Ab initio calculation of molecule-surface binding: methyl halides on GaAs(110) surfaces Surface Science. 382: 154-169. DOI: 10.1016/S0039-6028(97)00119-2 |
0.41 |
|
| 1997 |
Mainz DT, Klicic JJ, Friesner RA, Langlois JM, Perry JK. Extension of the PS-GVB electronic structure code to transition metal complexes Journal of Computational Chemistry. 18: 1863-1874. DOI: 10.1002/(Sici)1096-987X(19971130)18:15<1863::Aid-Jcc3>3.0.Co;2-M |
0.373 |
|
| 1997 |
Cortis CM, Friesner RA. Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes Journal of Computational Chemistry. 18: 1591-1608. DOI: 10.1002/(Sici)1096-987X(199710)18:13<1591::Aid-Jcc3>3.0.Co;2-M |
0.31 |
|
| 1996 |
Cortis CM, Langlois J, Beachy MD, Friesner RA. Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method The Journal of Chemical Physics. 105: 5472-5484. DOI: 10.1063/1.472388 |
0.36 |
|
| 1996 |
Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects The Journal of Physical Chemistry. 100: 11775-11788. DOI: 10.1021/Jp953087X |
0.571 |
|
| 1995 |
Murphy RB, Beachy MD, Friesner RA, Ringnalda MN. Pseudospectral localized Mo/ller–Plesset methods: Theory and calculation of conformational energies The Journal of Chemical Physics. 103: 1481-1490. DOI: 10.1063/1.469769 |
0.424 |
|
| 1995 |
Zhang LY, Friesner RA. Ab Initio Electronic Structure Calculation of the Redox Potentials of Bacteriochlorophyll and Bacteriopheophytin in Solution The Journal of Physical Chemistry. 99: 16479-16482. DOI: 10.1021/J100044A042 |
0.401 |
|
| 1995 |
Humphreys DD, Friesner RA, Berne BJ. Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics Journal of Physical Chemistry. 99: 10674-10685. DOI: 10.1021/J100026A035 |
0.497 |
|
| 1995 |
Zorman B, Ramakrishna MV, Friesner RA. Quantum Confinement Effects in CdSe Quantum Dots The Journal of Physical Chemistry. 99: 7649-7653. DOI: 10.1021/J100019A052 |
0.322 |
|
| 1994 |
Monge A, Friesner RA, Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 91: 5027-9. PMID 8197177 DOI: 10.1073/Pnas.91.11.5027 |
0.522 |
|
| 1994 |
Friesner RA. Comparison of theory and experiment for electron transfers in proteins: where's the beef? Structure (London, England : 1993). 2: 339-43. PMID 8081749 DOI: 10.1016/S0969-2126(00)00035-6 |
0.308 |
|
| 1994 |
Murphy RB, Friesner RA, Ringnalda MN, Goddard WA. Pseudospectral contracted configuration interaction from a generalized valence bond reference The Journal of Chemical Physics. 101: 2986-2994. DOI: 10.1063/1.467611 |
0.325 |
|
| 1994 |
Greeley BH, Russo TV, Mainz DT, Friesner RA, Langlois J, Goddard WA, Donnelly RE, Ringnalda MN. New pseudospectral algorithms for electronic structure calculations: Length scale separation and analytical two‐electron integral corrections The Journal of Chemical Physics. 101: 4028-4041. DOI: 10.1063/1.467520 |
0.797 |
|
| 1994 |
Pollard WT, Friesner RA. Solution of the Redfield equation for the dissipative quantum dynamics of multilevel systems The Journal of Chemical Physics. 100: 5054-5065. DOI: 10.1063/1.467222 |
0.304 |
|
| 1994 |
Webster F, Wang ET, Rossky PJ, Friesner RA. Stationary phase surface hopping for nonadiabatic dynamics: Two-state systems The Journal of Chemical Physics. 100: 4835-4847. DOI: 10.1063/1.467204 |
0.326 |
|
| 1994 |
Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Honig B, Ringnalda M, Goddard WA. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory Journal of the American Chemical Society. 116: 11875-11882. DOI: 10.1021/Ja00105A030 |
0.542 |
|
| 1994 |
Humphreys DD, Friesner RA, Berne BJ. A multiple-time-step Molecular Dynamics algorithm for macromolecules Journal of Physical Chemistry. 98: 6885-6892. DOI: 10.1021/J100078A035 |
0.511 |
|
| 1994 |
Gunn JR, Monge A, Friesner RA, Marshall CH. Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 .ANG. resolution The Journal of Physical Chemistry. 98: 702-711. DOI: 10.1021/J100053A053 |
0.361 |
|
| 1993 |
Pollard WT, Friesner RA. Efficient Fock matrix diagonalization by a Krylov‐space method The Journal of Chemical Physics. 99: 6742-6750. DOI: 10.1063/1.465817 |
0.307 |
|
| 1993 |
Friesner RA, Bentley JA, Menou M, Leforestier C. Adiabatic pseudospectral methods for multidimensional vibrational potentials The Journal of Chemical Physics. 99: 324-335. DOI: 10.1063/1.465810 |
0.351 |
|
| 1993 |
Lee JG, Friesner RA. Atomic charges for large molecules derived from electrostatic potentials: fragment density matrix approach The Journal of Physical Chemistry. 97: 3515-3519. DOI: 10.1021/J100116A013 |
0.307 |
|
| 1992 |
Jean JM, Friesner RA, Fleming GR. Application of a multilevel Redfield theory to electron transfer in condensed phases The Journal of Chemical Physics. 96: 5827-5842. DOI: 10.1063/1.462858 |
0.341 |
|
| 1992 |
Thiem H, Wiedenfeld DJ, Lee J, Friesner RA. AMBER force field parameters for the trimethylanilinium cation Bioorganic & Medicinal Chemistry Letters. 2: 291-294. DOI: 10.1016/S0960-894X(01)80202-X |
0.306 |
|
| 1991 |
Webster FJ, Schnitker J, Friedrichs MS, Friesner RA, Rossky PJ. Solvation dynamics of the hydrated electron: A nonadiabatic quantum simulation. Physical Review Letters. 66: 3172-3175. PMID 10043717 DOI: 10.1103/Physrevlett.66.3172 |
0.313 |
|
| 1991 |
Friesner RA. New methods for electronic structure calculations on large molecules. Annual Review of Physical Chemistry. 42: 341-67. PMID 1747190 DOI: 10.1146/Annurev.Pc.42.100191.002013 |
0.361 |
|
| 1991 |
Won Y, Lee J, Ringnalda MN, Friesner RA. Pseudospectral Hartree–Fock gradient calculations The Journal of Chemical Physics. 94: 8152-8157. DOI: 10.1063/1.460097 |
0.365 |
|
| 1991 |
Webster F, Rossky PJ, Friesner RA. Nonadiabatic processes in condensed matter: semi-classical theory and implementation Computer Physics Communications. 63: 494-522. DOI: 10.1016/0010-4655(91)90272-M |
0.301 |
|
| 1990 |
Ringnalda MN, Belhadj M, Friesner RA. Pseudospectral Hartree–Fock theory: Applications and algorithmic improvements The Journal of Chemical Physics. 93: 3397-3407. DOI: 10.1063/1.458819 |
0.363 |
|
| 1990 |
Langlois J, Muller RP, Coley TR, Goddard WA, Ringnalda MN, Won Y, Friesner RA. Pseudospectral generalized valence‐bond calculations: Application to methylene, ethylene, and silylene The Journal of Chemical Physics. 92: 7488-7497. DOI: 10.1063/1.458184 |
0.372 |
|
| 1990 |
Ringnalda MN, Won Y, Friesner RA. Pseudospectral Hartree–Fock calculations on glycine The Journal of Chemical Physics. 92: 1163-1173. DOI: 10.1063/1.458178 |
0.351 |
|
| 1989 |
Won Y, Friesner RA, Johnson MR, Sessler JL. Exciton interactions in synthetic porphyrin dimers. Photosynthesis Research. 22: 201-10. PMID 24424810 DOI: 10.1007/Bf00048299 |
0.358 |
|
| 1988 |
Friesner RA. An automatic grid generation scheme for pseudospectral self-consistent field calculations on polyatomic molecules The Journal of Physical Chemistry. 92: 3091-3096. DOI: 10.1021/J100322A017 |
0.341 |
|
| 1987 |
Lagos RE, Friesner RA. Green functions for anisotropic tight-binding hamiltonians: Application to exciton migration and optical lineshape Journal of Physics C: Solid State Physics. 20: 4833-4843. DOI: 10.1088/0022-3719/20/29/018 |
0.304 |
|
| 1987 |
Friesner RA. Solution of the Hartree–Fock equations for polyatomic molecules by a pseudospectral method The Journal of Chemical Physics. 86: 3522-3531. DOI: 10.1063/1.451955 |
0.352 |
|
| 1986 |
Moiseyev N, Friesner RA, Wyatt RE. Natural expansion of vibrational wave functions: RRGM with residue algebra The Journal of Chemical Physics. 85: 331-336. DOI: 10.1063/1.451660 |
0.331 |
|
| 1986 |
Friesner RA. Solution of the Hartree–Fock equations by a pseudospectral method: Application to diatomic molecules The Journal of Chemical Physics. 85: 1462-1468. DOI: 10.1063/1.451237 |
0.306 |
|
| 1986 |
Jean JM, Friesner RA. An accurate and efficient decoupling approximation for temperature‐dependent multimode resonance Raman spectra The Journal of Chemical Physics. 85: 2353-2364. DOI: 10.1063/1.451089 |
0.316 |
|
| 1986 |
Won Y, Lagos R, Friesner R. Numerical tests of a generalized multilevel vibronic coupling formalism The Journal of Chemical Physics. 84: 6567-6574. DOI: 10.1063/1.450709 |
0.328 |
|
| 1984 |
Lagos RE, Friesner RA. Cluster generalization of the dynamical coherent-potential approximation: Application to exciton-phonon interactions in molecular crystals Physical Review B. 29: 3045-3056. DOI: 10.1103/Physrevb.29.3045 |
0.311 |
|
| 1984 |
Calef DF, Friesner R, Korzeniewski G, Laird B, Silbey R. Calculation of the Green's function from high- and low-density series expansions for disordered transport Physical Review A. 29: 2963-2965. DOI: 10.1103/Physreva.29.2963 |
0.508 |
|
| 1984 |
Lagos RE, Friesner RA. Calculation of optical line shapes for generalized multilevel vibronic systems The Journal of Chemical Physics. 81: 5899-5905. DOI: 10.1063/1.447590 |
0.306 |
|
| 1984 |
Friesner RA, Levy RM. An optimized harmonic reference system for the evaluation of discretized path integrals The Journal of Chemical Physics. 80: 4488-4495. DOI: 10.1063/1.447232 |
0.326 |
|
| 1984 |
Dismukes G, Frank HA, Friesner R, Sauer K. Electronic interactions between iron and the bound semiquinones in bacterial photosynthesis. EPR spectroscopy of oriented cells of Rhodopseudomonas viridis Biochimica Et Biophysica Acta (Bba) - Bioenergetics. 764: 253-271. DOI: 10.1016/0005-2728(84)90096-3 |
0.635 |
|
| 1983 |
Frank HA, Machnicki J, Friesner R. ENERGY TRANSFER BETWEEN THE PRIMARY DONOR BACTERIOCHLOROPHYLL AND CAROTENOIDS IN Rhodopseudomonas sphaeroides Photochemistry and Photobiology. 38: 451-455. DOI: 10.1111/J.1751-1097.1983.Tb03365.X |
0.549 |
|
| 1983 |
Korzeniewski G, Friesner R, Silbey R. Localized excitation transport on substitutionally disordered lattices Journal of Statistical Physics. 31: 451-465. DOI: 10.1007/Bf01019493 |
0.486 |
|
| 1982 |
Friesner R, Silbey R. Calculation of the exciton green's function of a molecular crystal from a two-site dynamical coherent potential approximation Chemical Physics Letters. 93: 107-110. DOI: 10.1016/0009-2614(82)83674-9 |
0.523 |
|
| 1981 |
Nairn JA, Friesner R, Frank HA, Sauer K. A new approach to the theory of linear dichroism in partially ordered systems. Application to reaction centers and whole cells of photosynthetic bacteria. Biophysical Journal. 32: 733-53. PMID 7020787 DOI: 10.1016/S0006-3495(80)85013-2 |
0.75 |
|
| 1981 |
Friesner RA, Silbey R. Linear vibronic coupling in a general two level system The Journal of Chemical Physics. 75: 3925-3936. DOI: 10.1063/1.442549 |
0.527 |
|
| 1981 |
Friesner R, Silbey R. Absorption and circular dichroism line shapes of a molecular dimer in the strong electronic coupling limit The Journal of Chemical Physics. 75: 5630-5639. DOI: 10.1063/1.442002 |
0.522 |
|
| 1981 |
Friesner R, Silbey R. Exciton–phonon coupling in a dimer: An analytic approximation for eigenvalues and eigenvectors The Journal of Chemical Physics. 74: 1166-1174. DOI: 10.1063/1.441224 |
0.512 |
|
| 1981 |
Nairn JA, Friesner R, Sauer K. A general theory of the spectroscopic properties of partially ordered ensembles. II. Two‐vector problems The Journal of Chemical Physics. 74: 5398-5406. DOI: 10.1063/1.440942 |
0.689 |
|
| 1981 |
Friesner R, McCracken JL, Sauer K. Transient solutions of the bloch equations for inhomogeneously broadened lines Journal of Magnetic Resonance (1969). 43: 343-356. DOI: 10.1016/0022-2364(81)90047-0 |
0.651 |
|
| 1981 |
Friesner R, Silbey R. Effect of inhomogeneous broadening on the optical line shape of molecular aggregates Chemical Physics Letters. 84: 365-369. DOI: 10.1016/0009-2614(81)80365-X |
0.479 |
|
| 1979 |
Friesner R, Dismukes GC, Sauer K. Development of electron spin polarization in photosynthetic electron transfer by the radical pair mechanism. Biophysical Journal. 25: 277-94. PMID 233573 DOI: 10.1016/S0006-3495(79)85291-1 |
0.524 |
|
| 1979 |
Frank HA, Bolt J, Friesner R, Sauer K. Magnetophotoselection of the triplet state of reaction centers from Rhodopseudomonas sphaeroides R-26. Biochimica Et Biophysica Acta. 547: 502-11. PMID 226130 DOI: 10.1016/0005-2728(79)90030-6 |
0.645 |
|
| 1979 |
Frank HA, Friesner R, Nairn JA, Dismukes GC, Sauer K. The orientation of the primary donor in bacterial photosynthesis. Biochimica Et Biophysica Acta. 547: 484-501. PMID 226129 DOI: 10.1016/0005-2728(79)90029-X |
0.733 |
|
| 1979 |
Friesner R, Nairn JA, Sauer K. Direct calculation of the orientational distribution function of partially ordered ensembles from the EPR line shape The Journal of Chemical Physics. 71: 358-365. DOI: 10.1063/1.438078 |
0.677 |
|
| 1979 |
Dismukes C, McGuire A, Friesner R, Sauer K. Electron spin polarization from the photosynthetic light reaction: Photosystem I Reviews of Chemical Intermediates. 3: 59-88. DOI: 10.1007/Bf03052281 |
0.518 |
|
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