| Year |
Citation |
Score |
| 2024 |
Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical Science. 15: 12861-12878. PMID 39148808 DOI: 10.1039/d4sc00690a |
0.656 |
|
| 2024 |
Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The Journal of Physical Chemistry. B. PMID 38989715 DOI: 10.1021/acs.jpcb.4c01558 |
0.306 |
|
| 2024 |
Hahn DF, Gapsys V, de Groot BL, Mobley DL, Tresadern G. Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. Journal of Chemical Information and Modeling. 64: 5063-5076. PMID 38895959 DOI: 10.1021/acs.jcim.4c00417 |
0.438 |
|
| 2024 |
Baumann HM, Mobley DL. Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. Journal of Computational Chemistry. PMID 38725239 DOI: 10.1002/jcc.27365 |
0.357 |
|
| 2024 |
Amezcua M, Setiadi J, Mobley DL. The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy. Physical Chemistry Chemical Physics : Pccp. 26: 9207-9225. PMID 38444308 DOI: 10.1039/d3cp05111k |
0.381 |
|
| 2024 |
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model. Journal of Chemical Theory and Computation. PMID 38291966 DOI: 10.1021/acs.jctc.3c00870 |
0.359 |
|
| 2024 |
Wang L, Schauperl M, Mobley DL, Bayly C, Gilson MK. A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 38240687 DOI: 10.1021/acs.jctc.3c01171 |
0.36 |
|
| 2023 |
Horton JT, Boothroyd S, Behara PK, Mobley DL, Cole DJ. A transferable double exponential potential for condensed phase simulations of small molecules. Digital Discovery. 2: 1178-1187. PMID 38013814 DOI: 10.1039/d3dd00070b |
0.343 |
|
| 2023 |
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM. Biorxiv : the Preprint Server For Biology. PMID 37503302 DOI: 10.1101/2023.07.14.549110 |
0.358 |
|
| 2023 |
Baumann HM, Dybeck E, McClendon CL, Pickard FC, Gapsys V, Pérez-Benito L, Hahn DF, Tresadern G, Mathiowetz AM, Mobley DL. Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach. Journal of Chemical Theory and Computation. PMID 37487138 DOI: 10.1021/acs.jctc.3c00282 |
0.386 |
|
| 2023 |
Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, ... ... Mobley DL, et al. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation. PMID 37167319 DOI: 10.1021/acs.jctc.3c00039 |
0.643 |
|
| 2023 |
Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 36692215 DOI: 10.1021/acs.jctc.2c00823 |
0.509 |
|
| 2022 |
D'Amore L, Hahn DF, Dotson DL, Horton JT, Anwar J, Craig I, Fox T, Gobbi A, Lakkaraju SK, Lucas X, Meier K, Mobley DL, Narayanan A, Schindler CEM, Swope WC, et al. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. Journal of Chemical Information and Modeling. PMID 36433835 DOI: 10.1021/acs.jcim.2c01185 |
0.35 |
|
| 2022 |
Hahn DF, Bayly CI, Macdonald HEB, Chodera JD, Mey ASJS, Mobley DL, Benito LP, Schindler CEM, Tresadern G, Warren GL. Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. Living Journal of Computational Molecular Science. 4. PMID 36382113 DOI: 10.33011/livecoms.4.1.1497 |
0.614 |
|
| 2022 |
Horton JT, Boothroyd S, Wagner J, Mitchell JA, Gokey T, Dotson DL, Behara PK, Ramaswamy VK, Mackey M, Chodera JD, Anwar J, Mobley DL, Cole DJ. Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. Journal of Chemical Information and Modeling. PMID 36351167 DOI: 10.1021/acs.jcim.2c01153 |
0.644 |
|
| 2022 |
Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. Prioritizing small sets of molecules for synthesis through in-silico tools: A comparison of common ranking methods. Chemmedchem. PMID 36240514 DOI: 10.1002/cmdc.202200425 |
0.543 |
|
| 2022 |
Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host-guest binding challenge. Journal of Computer-Aided Molecular Design. PMID 36229622 DOI: 10.1007/s10822-022-00462-5 |
0.575 |
|
| 2022 |
Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. Journal of Computer-Aided Molecular Design. PMID 36198874 DOI: 10.1007/s10822-022-00479-w |
0.492 |
|
| 2022 |
Ge Y, Baumann HM, Mobley DL. Absolute Binding Free Energy Calculations for Buried Water Molecules. Journal of Chemical Theory and Computation. PMID 36197451 DOI: 10.1021/acs.jctc.2c00658 |
0.582 |
|
| 2022 |
Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of Chemical Theory and Computation. PMID 35533269 DOI: 10.1021/acs.jctc.1c01268 |
0.619 |
|
| 2022 |
Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of Chemical Theory and Computation. PMID 35507313 DOI: 10.1021/acs.jctc.1c01111 |
0.627 |
|
| 2022 |
Grosjean H, Işık M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC. SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. Journal of Computer-Aided Molecular Design. PMID 35426591 DOI: 10.1007/s10822-022-00452-7 |
0.598 |
|
| 2022 |
Gapsys V, Hahn DF, Tresadern G, Mobley DL, Rampp M, de Groot BL. Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. Journal of Chemical Information and Modeling. PMID 35191702 DOI: 10.1021/acs.jcim.1c01445 |
0.348 |
|
| 2022 |
Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. Journal of Chemical Theory and Computation. PMID 35148093 DOI: 10.1021/acs.jctc.1c00590 |
0.502 |
|
| 2021 |
Bahr MN, Nandkeolyar A, Kenna JK, Nevins N, Da Vià L, Işık M, Chodera JD, Mobley DL. Automated high throughput pK and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. Journal of Computer-Aided Molecular Design. 35: 1141-1155. PMID 34714468 DOI: 10.1007/s10822-021-00427-0 |
0.626 |
|
| 2021 |
Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science. 12: 11275-11293. PMID 34667539 DOI: 10.1039/d1sc02751d |
0.499 |
|
| 2021 |
Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, ... ... Mobley DL, et al. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of Chemical Theory and Computation. PMID 34551262 DOI: 10.1021/acs.jctc.1c00571 |
0.801 |
|
| 2021 |
Baumann HM, Gapsys V, de Groot BL, Mobley DL. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. The Journal of Physical Chemistry. B. PMID 33905257 DOI: 10.1021/acs.jpcb.0c10263 |
0.369 |
|
| 2021 |
Ge Y, Hahn DF, Mobley DL. A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. Journal of Chemical Information and Modeling. PMID 33686853 DOI: 10.1021/acs.jcim.0c01424 |
0.592 |
|
| 2021 |
Ehrman JN, Lim VT, Bannan CC, Thi N, Kyu DY, Mobley DL. Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. Journal of Computer-Aided Molecular Design. PMID 33506360 DOI: 10.1007/s10822-020-00367-1 |
0.806 |
|
| 2021 |
Işık M, Rustenburg AS, Rizzi A, Gunner MR, Mobley DL, Chodera JD. Overview of the SAMPL6 pK challenge: evaluating small molecule microscopic and macroscopic pK predictions. Journal of Computer-Aided Molecular Design. PMID 33394238 DOI: 10.1007/s10822-020-00362-6 |
0.618 |
|
| 2021 |
Amezcua M, El Khoury L, Mobley DL. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 33392951 DOI: 10.1007/s10822-020-00363-5 |
0.351 |
|
| 2020 |
Mey ASJS, Allen BK, Macdonald HEB, Chodera JD, Hahn DF, Kuhn M, Michel J, Mobley DL, Naden LN, Prasad S, Rizzi A, Scheen J, Shirts MR, Tresadern G, Xu H. Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living Journal of Computational Molecular Science. 2. PMID 34458687 DOI: 10.33011/livecoms.2.1.18378 |
0.657 |
|
| 2020 |
Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000research. 9. PMID 33604023 DOI: 10.12688/f1000research.27141.1 |
0.796 |
|
| 2020 |
Ray D, Gokey T, Mobley DL, Andricioaei I. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning. The Journal of Chemical Physics. 153: 154117. PMID 33092382 DOI: 10.1063/5.0021953 |
0.362 |
|
| 2020 |
Lim VT, Geragotelis AD, Lim NM, Freites JA, Tombola F, Mobley DL, Tobias DJ. Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations. Scientific Reports. 10: 13587. PMID 32788614 DOI: 10.1038/S41598-020-70369-4 |
0.805 |
|
| 2020 |
Lim NM, Osato M, Warren GL, Mobley DL. Fragment pose prediction using non-equilibrium candidate Monte Carlo and molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 32167763 DOI: 10.1021/Acs.Jctc.9B01096 |
0.425 |
|
| 2020 |
Işık M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. Journal of Computer-Aided Molecular Design. PMID 32107702 DOI: 10.1007/S10822-020-00295-0 |
0.62 |
|
| 2020 |
Sasmal S, Gill SC, Lim NM, Mobley DL. Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 32058713 DOI: 10.1021/Acs.Jctc.9B01066 |
0.405 |
|
| 2020 |
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, ... Mobley DL, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5 |
0.72 |
|
| 2019 |
Işık M, Levorse D, Mobley DL, Rhodes T, Chodera JD. Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. Journal of Computer-Aided Molecular Design. PMID 31858363 DOI: 10.1007/S10822-019-00271-3 |
0.634 |
|
| 2019 |
Sasmal S, El Khoury L, Mobley DL. D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. Journal of Computer-Aided Molecular Design. PMID 31781990 DOI: 10.1007/S10822-019-00249-1 |
0.447 |
|
| 2019 |
Yang Q, Burchett W, Steeno GS, Liu S, Yang M, Mobley DL, Hou X. Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. Journal of Computational Chemistry. PMID 31721260 DOI: 10.1002/Jcc.26095 |
0.463 |
|
| 2019 |
El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31691919 DOI: 10.1007/S10822-019-00240-W |
0.418 |
|
| 2019 |
Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M. Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of Chemical Theory and Computation. PMID 31603667 DOI: 10.1021/Acs.Jctc.9B00748 |
0.716 |
|
| 2019 |
Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C. Binding modes and metabolism of caffeine. Chemical Research in Toxicology. PMID 31132250 DOI: 10.1021/Acs.Chemrestox.9B00030 |
0.393 |
|
| 2019 |
Duarte Ramos Matos G, Calabró G, Mobley DL. Infinite dilution activity coefficients as constraints for force field parameterization and method development. Journal of Chemical Theory and Computation. PMID 30939010 DOI: 10.1021/Acs.Jctc.8B01029 |
0.819 |
|
| 2019 |
Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. Journal of the American Chemical Society. PMID 30834751 DOI: 10.1021/Jacs.8B13613 |
0.359 |
|
| 2019 |
Pellegrino S, Meyer M, Könst ZA, Holm M, Voora VK, Kashinskaya D, Zanette C, Mobley DL, Yusupova G, Vanderwal CD, Blanchard SC, Yusupov M. Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome. Nucleic Acids Research. PMID 30759226 DOI: 10.1093/Nar/Gkz053 |
0.318 |
|
| 2019 |
Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL. Assessing the conformational equilibrium of carboxylic acid via QM and MD studies on acetic acid. Journal of Chemical Information and Modeling. PMID 30742770 DOI: 10.1021/Acs.Jcim.8B00835 |
0.762 |
|
| 2019 |
Burley KH, Gill SC, Lim NM, Mobley DL. Enhancing Sidechain Rotamer Sampling Using Non-Equilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 30677291 DOI: 10.1021/Acs.Jctc.8B01018 |
0.436 |
|
| 2019 |
Lim VT, Lim NM, Geragotelis AD, Freites JA, Tombola F, Mobley DL, Tobias DJ. Computational Insights on Small Molecule Binding to the Hv1 Proton Channel Biophysical Journal. 116: 432a. DOI: 10.1016/J.Bpj.2018.11.2326 |
0.785 |
|
| 2018 |
Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward learned chemical perception of force field typing rules. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/Acs.Jctc.8B00821 |
0.799 |
|
| 2018 |
Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of Computer-Aided Molecular Design. PMID 30415285 DOI: 10.1007/S10822-018-0170-6 |
0.678 |
|
| 2018 |
Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD. pK measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. Journal of Computer-Aided Molecular Design. PMID 30406372 DOI: 10.1007/S10822-018-0168-0 |
0.642 |
|
| 2018 |
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Eastman PK. Escaping atom types in force fields using direct chemical perception. Journal of Chemical Theory and Computation. PMID 30351006 DOI: 10.1021/Acs.Jctc.8B00640 |
0.783 |
|
| 2018 |
Bannan CC, Mobley DL, Skillman AG. SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model. Journal of Computer-Aided Molecular Design. PMID 30324305 DOI: 10.1007/S10822-018-0169-Z |
0.799 |
|
| 2018 |
Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software. Journal of Chemical Theory and Computation. PMID 30289712 DOI: 10.1021/Acs.Jctc.8B00544 |
0.806 |
|
| 2018 |
Riquelme M, Lara A, Mobley DL, Verstraelen T, Matamala AR, Vöhringer-Martinez E. Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. Journal of Chemical Information and Modeling. PMID 30125107 DOI: 10.1021/Acs.Jcim.8B00180 |
0.495 |
|
| 2018 |
Duarte Ramos Matos G, Mobley DL. Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000research. 7: 686. PMID 30109026 DOI: 10.12688/F1000Research.14960.2 |
0.807 |
|
| 2018 |
Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS. Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. The Journal of Membrane Biology. PMID 29550876 DOI: 10.1007/S00232-018-0030-2 |
0.543 |
|
| 2018 |
Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. The Journal of Physical Chemistry. B. PMID 29486559 DOI: 10.1021/Acs.Jpcb.7B11820 |
0.64 |
|
| 2018 |
Yang X, Lei H, Gao P, Thomas DG, Mobley DL, Baker NA. Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations. Journal of Chemical Theory and Computation. PMID 29293342 DOI: 10.1021/Acs.Jctc.7B00905 |
0.444 |
|
| 2017 |
Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. Journal of Chemical and Engineering Data. 62: 1559-1569. PMID 29056756 DOI: 10.1021/Acs.Jced.7B00104 |
0.681 |
|
| 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 |
0.5 |
|
| 2017 |
Mobley DL, Gilson MK. Predicting Binding Free Energies. Annual Review of Biophysics. PMID 28399632 DOI: 10.1146/Annurev-Biophys-070816-033654 |
0.503 |
|
| 2016 |
Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA. Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free Energies. The Journal of Physical Chemistry. B. PMID 27966363 DOI: 10.1021/Acs.Jpcb.6B09198 |
0.43 |
|
| 2016 |
Evoli S, Mobley DL, Guzzi R, Rizzuti B. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations. Physical Chemistry Chemical Physics : Pccp. PMID 27854368 DOI: 10.1039/C6Cp05680F |
0.432 |
|
| 2016 |
Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/S10822-016-9977-1 |
0.429 |
|
| 2016 |
Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. PMID 27718028 DOI: 10.1007/S10822-016-9971-7 |
0.625 |
|
| 2016 |
Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. 30: 927-944. PMID 27677750 DOI: 10.1007/S10822-016-9954-8 |
0.803 |
|
| 2016 |
Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? Journal of Computer-Aided Molecular Design. PMID 27658802 DOI: 10.1007/S10822-016-9974-4 |
0.485 |
|
| 2016 |
Lim NM, Wang L, Abel R, Mobley DL. Sensitivity in binding free energies due to protein reorganization. Journal of Chemical Theory and Computation. PMID 27462935 DOI: 10.1021/Acs.Jctc.6B00532 |
0.439 |
|
| 2016 |
Bannan CC, Calabro G, Kyu DY, Mobley DL. Calculating partition coefficients of small molecules in octanol/water and cyclohexane/water. Journal of Chemical Theory and Computation. PMID 27434695 DOI: 10.1021/Acs.Jctc.6B00449 |
0.816 |
|
| 2016 |
Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. Using MD simulations to calculate how solvents modulate solubility. Journal of Chemical Theory and Computation. PMID 26878198 DOI: 10.1021/Acs.Jctc.5B00934 |
0.426 |
|
| 2016 |
Mobley DL, Abel R, Wang L, Lim N. Examining how protein sampling impacts the convergence of relative binding free energy calculations F1000research. 5. DOI: 10.7490/F1000Research.1111982.1 |
0.424 |
|
| 2015 |
Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. Journal of Chemical Theory and Computation. 11: 1347. PMID 26579779 DOI: 10.1021/Acs.Jctc.5B00154 |
0.583 |
|
| 2015 |
Klimovich PV, Mobley DL. A Python tool to set up relative free energy calculations in GROMACS. Journal of Computer-Aided Molecular Design. 29: 1007-14. PMID 26487189 DOI: 10.1007/S10822-015-9873-0 |
0.491 |
|
| 2015 |
Liu S, Wang L, Mobley DL. Is ring breaking feasible in relative binding free energy calculations? Journal of Chemical Information and Modeling. 55: 727-35. PMID 25835054 DOI: 10.1021/Acs.Jcim.5B00057 |
0.456 |
|
| 2015 |
Klimovich PV, Shirts MR, Mobley DL. Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design. 29: 397-411. PMID 25808134 DOI: 10.1007/S10822-015-9840-9 |
0.453 |
|
| 2015 |
Paluch AS, Parameswaran S, Liu S, Kolavennu A, Mobley DL. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation. The Journal of Chemical Physics. 142: 044508. PMID 25637996 DOI: 10.1063/1.4906491 |
0.447 |
|
| 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, ... ... Mobley DL, 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 |
0.504 |
|
| 2014 |
Parameswaran S, Mobley DL. Box size effects are negligible for solvation free energies of neutral solutes. Journal of Computer-Aided Molecular Design. 28: 825-9. PMID 24976043 DOI: 10.1007/S10822-014-9766-7 |
0.462 |
|
| 2014 |
Mobley DL, Guthrie JP. FreeSolv: a database of experimental and calculated hydration free energies, with input files. Journal of Computer-Aided Molecular Design. 28: 711-20. PMID 24928188 DOI: 10.1007/S10822-014-9747-X |
0.459 |
|
| 2014 |
Fennell CJ, Wymer KL, Mobley DL. A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration Journal of Physical Chemistry B. 118: 6438-6446. PMID 24702668 DOI: 10.1021/Jp411529H |
0.749 |
|
| 2014 |
Mobley DL, Wymer KL, Lim NM, Guthrie JP. Blind prediction of solvation free energies from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 135-50. PMID 24615156 DOI: 10.1007/S10822-014-9718-2 |
0.511 |
|
| 2014 |
Muddana HS, Fenley AT, Mobley DL, Gilson MK. The SAMPL4 host-guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design. 28: 305-17. PMID 24599514 DOI: 10.1007/S10822-014-9735-1 |
0.46 |
|
| 2014 |
Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. Blind prediction of HIV integrase binding from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 327-45. PMID 24595873 DOI: 10.1007/S10822-014-9723-5 |
0.395 |
|
| 2014 |
Peat TS, Dolezal O, Newman J, Mobley D, Deadman JJ. Interrogating HIV integrase for compounds that bind--a SAMPL challenge. Journal of Computer-Aided Molecular Design. 28: 347-62. PMID 24532034 DOI: 10.1007/S10822-014-9721-7 |
0.315 |
|
| 2014 |
Mobley DL, Rocklin GJ. Predicting Charged-Ligand Binding from Molecular Simulations Biophysical Journal. 106: 250a. DOI: 10.1016/J.Bpj.2013.11.1462 |
0.782 |
|
| 2013 |
Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. The Journal of Chemical Physics. 139: 184103. PMID 24320250 DOI: 10.1063/1.4826261 |
0.802 |
|
| 2013 |
Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. Lead optimization mapper: automating free energy calculations for lead optimization. Journal of Computer-Aided Molecular Design. 27: 755-70. PMID 24072356 DOI: 10.1007/S10822-013-9678-Y |
0.434 |
|
| 2013 |
Rocklin GJ, Mobley DL, Dill KA. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. Journal of Chemical Theory and Computation. 9: 3072-3083. PMID 24015114 DOI: 10.1021/Ct400315Q |
0.821 |
|
| 2013 |
Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. Journal of Molecular Biology. 425: 4569-83. PMID 23896298 DOI: 10.1016/J.Jmb.2013.07.030 |
0.806 |
|
| 2013 |
Chodera JD, Mobley DL. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annual Review of Biophysics. 42: 121-42. PMID 23654303 DOI: 10.1146/Annurev-Biophys-083012-130318 |
0.642 |
|
| 2013 |
Rocklin GJ, Mobley DL, Dill KA. Separated topologies--a method for relative binding free energy calculations using orientational restraints. The Journal of Chemical Physics. 138: 085104. PMID 23464180 DOI: 10.1063/1.4792251 |
0.813 |
|
| 2013 |
Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods in Molecular Biology (Clifton, N.J.). 924: 271-311. PMID 23034753 DOI: 10.1007/978-1-62703-017-5_11 |
0.509 |
|
| 2013 |
Klimovich PV, Mobley DL. Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations Journal of Computer-Aided Molecular Design. 27: 105-105. DOI: 10.1007/s10822-012-9622-6 |
0.333 |
|
| 2012 |
Mobley DL, Klimovich PV. Perspective: Alchemical free energy calculations for drug discovery. The Journal of Chemical Physics. 137: 230901. PMID 23267463 DOI: 10.1063/1.4769292 |
0.467 |
|
| 2012 |
Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. Alchemical prediction of hydration free energies for SAMPL. Journal of Computer-Aided Molecular Design. 26: 551-62. PMID 22198475 DOI: 10.1007/S10822-011-9528-8 |
0.486 |
|
| 2012 |
Mobley DL. Let's get honest about sampling. Journal of Computer-Aided Molecular Design. 26: 93-5. PMID 22113833 DOI: 10.1007/S10822-011-9497-Y |
0.448 |
|
| 2011 |
Paluch AS, Mobley DL, Maginn EJ. Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. 7: 2910-8. PMID 26605480 DOI: 10.1021/Ct200377W |
0.485 |
|
| 2011 |
Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology. 21: 150-60. PMID 21349700 DOI: 10.1016/J.Sbi.2011.01.011 |
0.628 |
|
| 2011 |
Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. Correction to “Charge Asymmetries in Hydration of Polar Solutes” The Journal of Physical Chemistry B. 115: 15145-15145. DOI: 10.1021/Jp210487K |
0.707 |
|
| 2010 |
Klimovich PV, Mobley DL. Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. Journal of Computer-Aided Molecular Design. 24: 307-16. PMID 20372973 DOI: 10.1007/S10822-010-9343-7 |
0.527 |
|
| 2010 |
Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D |
0.711 |
|
| 2009 |
McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 5: 2486-2502. PMID 20161451 DOI: 10.1021/Ct9001812 |
0.359 |
|
| 2009 |
Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. Journal of Chemical Theory and Computation. 5: 350-358. PMID 20150953 DOI: 10.1021/Ct800409D |
0.653 |
|
| 2009 |
Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. Journal of Molecular Biology. 394: 747-63. PMID 19782087 DOI: 10.1016/J.Jmb.2009.09.049 |
0.818 |
|
| 2009 |
Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (London, England : 1993). 17: 489-98. PMID 19368882 DOI: 10.1016/J.Str.2009.02.010 |
0.575 |
|
| 2009 |
Mobley DL, Bayly CI, Cooper MD, Dill KA. Predictions of hydration free energies from all-atom molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 4533-7. PMID 19271713 DOI: 10.1021/Jp806838B |
0.63 |
|
| 2008 |
Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. Charge asymmetries in hydration of polar solutes. The Journal of Physical Chemistry. B. 112: 2405-14. PMID 18251538 DOI: 10.1021/Jp709958F |
0.737 |
|
| 2008 |
Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. Journal of Medicinal Chemistry. 51: 769-79. PMID 18215013 DOI: 10.1021/Jm070549+ |
0.686 |
|
| 2008 |
Mobley DL, Dill KA, Chodera JD. Treating entropy and conformational changes in implicit solvent simulations of small molecules. The Journal of Physical Chemistry. B. 112: 938-46. PMID 18171044 DOI: 10.1021/Jp0764384 |
0.721 |
|
| 2007 |
Mobley DL, Chodera JD, Dill KA. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation. 3: 1231-1235. PMID 18843379 DOI: 10.1021/Ct700032N |
0.731 |
|
| 2007 |
Steinbrecher T, Mobley DL, Case DA. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. The Journal of Chemical Physics. 127: 214108. PMID 18067350 DOI: 10.1063/1.2799191 |
0.423 |
|
| 2007 |
Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. The Journal of Physical Chemistry. B. 111: 13052-63. PMID 17949030 DOI: 10.1021/Jp0735987 |
0.678 |
|
| 2007 |
Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology. 371: 1118-34. PMID 17599350 DOI: 10.1016/J.Jmb.2007.06.002 |
0.747 |
|
| 2007 |
Mobley DL, Dumont E, Chodera JD, Dill KA. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. The Journal of Physical Chemistry. B. 111: 2242-54. PMID 17291029 DOI: 10.1021/Jp0667442 |
0.745 |
|
| 2007 |
Shirts MR, Mobley DL, Chodera JD. Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? Annual Reports in Computational Chemistry. 3: 41-59. DOI: 10.1016/S1574-1400(07)03004-6 |
0.681 |
|
| 2006 |
Mobley DL, Chodera JD, Dill KA. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. The Journal of Chemical Physics. 125: 084902. PMID 16965052 DOI: 10.1063/1.2221683 |
0.737 |
|
| 2004 |
Mobley DL, Cox DL, Singh RR, Maddox MW, Longo ML. Modeling amyloid beta-peptide insertion into lipid bilayers. Biophysical Journal. 86: 3585-97. PMID 15189856 DOI: 10.1529/Biophysj.103.032342 |
0.657 |
|
| 2004 |
Mobley DL, Pike CR, Davies JE, Cox DL, Singh RRP. Hysteresis loops of Co–Pt perpendicular magnetic multilayers Journal of Physics: Condensed Matter. 16: 5897-5906. DOI: 10.1088/0953-8984/16/32/022 |
0.55 |
|
| 2003 |
Mobley DL, Cox DL, Singh RR, Kulkarni RV, Slepoy A. Simulations of oligomeric intermediates in prion diseases. Biophysical Journal. 85: 2213-23. PMID 14507687 DOI: 10.1016/S0006-3495(03)74647-5 |
0.673 |
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