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The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy. Phys Chem Chem Phys. 2024 Mar 06.
Amezcua M, Setiadi J, Mobley DL. PMID: 38444308.
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PubMed Mentions: Fields:
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PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model. J Chem Theory Comput. 2024 Feb 13; 20(3):1036-1050.
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PMID: 38291966; PMCID: PMC10867841.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. J Chem Theory Comput. 2024 Feb 13; 20(3):1293-1305.
Wang L, Schauperl M, Mobley DL, Bayly C, Gilson MK. PMID: 38240687; PMCID: PMC10867846.
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PubMed Mentions: Fields:
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Building Block-Based Binding Predictions for DNA-Encoded Libraries. J Chem Inf Model. 2023 08 28; 63(16):5120-5132.
Zhang C, Pitman M, Dixit A, Leelananda S, Palacci H, Lawler M, Belyanskaya S, Grady L, Franklin J, Tilmans N, Mobley DL. PMID: 37578123; PMCID: PMC10466377.
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PubMed Mentions: Fields:
-
PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM. bioRxiv. 2023 Aug 08.
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PMID: 37503302; PMCID: PMC10370083.
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PubMed Mentions:
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Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach. J Chem Theory Comput. 2023 Aug 08; 19(15):5058-5076.
Baumann HM, Dybeck E, McClendon CL, Pickard FC, Gapsys V, Pérez-Benito L, Hahn DF, Tresadern G, Mathiowetz AM, Mobley DL. PMID: 37487138; PMCID: PMC10413862.
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PubMed Mentions:
4 Fields:
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A transferable double exponential potential for condensed phase simulations of small molecules. Digit Discov. 2023 Aug 08; 2(4):1178-1187.
Horton JT, Boothroyd S, Behara PK, Mobley DL, Cole DJ. PMID: 38013814; PMCID: PMC10408570.
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PubMed Mentions:
3
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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. J Chem Theory Comput. 2023 Jun 13; 19(11):3251-3275.
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, Chodera JD, Bayly CI, Shirts MR, Mobley DL. PMID: 37167319; PMCID: PMC10269353.
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PubMed Mentions:
16 Fields:
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To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. J Chem Inf Model. 2023 03 27; 63(6):1776-1793.
Pitman M, Hahn DF, Tresadern G, Mobley DL. PMID: 36878475; PMCID: PMC10547263.
View in:
PubMed Mentions:
3 Fields:
Translation:
Cells
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Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo. J Chem Theory Comput. 2023 Feb 14; 19(3):1050-1062.
Melling OJ, Samways ML, Ge Y, Mobley DL, Essex JW. PMID: 36692215; PMCID: PMC9933432.
View in:
PubMed Mentions:
3 Fields:
-
Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol. 2023 Jan 01; 79(Pt 1):50-65.
Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. PMID: 36601807; PMCID: PMC9815100.
View in:
PubMed Mentions:
5 Translation:
Cells
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Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods. ChemMedChem. 2023 01 03; 18(1):e202200425.
Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. PMID: 36240514; PMCID: PMC9868080.
View in:
PubMed Mentions:
18 Fields:
Translation:
Cells
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Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J Chem Inf Model. 2022 Nov 26.
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, In 't Veld PJ, Wagner J, Xue B, Tresadern G. PMID: 36433835.
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PubMed Mentions:
4 Fields:
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Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. J Chem Inf Model. 2022 11 28; 62(22):5622-5633.
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. PMID: 36351167; PMCID: PMC9709916.
View in:
PubMed Mentions:
6 Fields:
Translation:
Cells
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An overview of the SAMPL8 host-guest binding challenge. J Comput Aided Mol Des. 2022 10; 36(10):707-734.
Amezcua M, Setiadi J, Ge Y, Mobley DL. PMID: 36229622; PMCID: PMC9596595.
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PubMed Mentions:
10 Fields:
Translation:
HumansCells
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Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. J Comput Aided Mol Des. 2022 10; 36(10):767-779.
Ge Y, Melling OJ, Dong W, Essex JW, Mobley DL. PMID: 36198874; PMCID: PMC9869699.
View in:
PubMed Mentions:
2 Fields:
Translation:
Cells
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Absolute Binding Free Energy Calculations for Buried Water Molecules. J Chem Theory Comput. 2022 Nov 08; 18(11):6482-6499.
Ge Y, Baumann HM, Mobley DL. PMID: 36197451; PMCID: PMC9873352.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. Living J Comput Mol Sci. 2022; 4(1).
Hahn DF, Bayly CI, Macdonald HEB, Chodera JD, Mey ASJS, Mobley DL, Benito LP, Schindler CEM, Tresadern G, Warren GL. PMID: 36382113; PMCID: PMC9662604.
View in:
PubMed Mentions:
18
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Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput. 2022 Jun 14; 18(6):3577-3592.
Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. PMID: 35533269; PMCID: PMC9254460.
View in:
PubMed Mentions:
6 Fields:
-
Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. J Chem Theory Comput. 2022 Jun 14; 18(6):3566-3576.
Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. PMID: 35507313; PMCID: PMC9245177.
View in:
PubMed Mentions:
7 Fields:
Translation:
Humans
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SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J Comput Aided Mol Des. 2022 04; 36(4):291-311.
Grosjean H, Isik M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC. PMID: 35426591; PMCID: PMC9010448.
View in:
PubMed Mentions:
4 Fields:
Translation:
Cells
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Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J Chem Inf Model. 2022 03 14; 62(5):1172-1177.
Gapsys V, Hahn DF, Tresadern G, Mobley DL, Rampp M, de Groot BL. PMID: 35191702; PMCID: PMC8924919.
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PubMed Mentions:
13 Fields:
Translation:
Cells
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Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. J Chem Theory Comput. 2022 Mar 08; 18(3):1359-1381.
Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. PMID: 35148093; PMCID: PMC9241631.
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PubMed Mentions:
14 Fields:
Translation:
Cells
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Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site. Int J Mol Sci. 2021 Nov 23; 22(23).
El Khoury L, Mobley DL, Ye D, Rempe SB. PMID: 34884430; PMCID: PMC8657610.
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PubMed Mentions: Fields:
Translation:
Cells
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Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. J Comput Aided Mol Des. 2021 11; 35(11):1141-1155.
Bahr MN, Nandkeolyar A, Kenna JK, Nevins N, Da Vià L, Isik M, Chodera JD, Mobley DL. PMID: 34714468; PMCID: PMC9313606.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Alchemical absolute protein-ligand binding free energies for drug design. Chem Sci. 2021 Oct 27; 12(41):13958-13971.
Khalak Y, Tresadern G, Aldeghi M, Baumann HM, Mobley DL, de Groot BL, Gapsys V. PMID: 34760182; PMCID: PMC8549785.
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PubMed Mentions:
21
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Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput. 2021 Oct 12; 17(10):6262-6280.
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, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. PMID: 34551262; PMCID: PMC8511297.
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PubMed Mentions:
52 Fields:
Translation:
HumansAnimalsCells
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Temperature artifacts in protein structures bias ligand-binding predictions. Chem Sci. 2021 Sep 01; 12(34):11275-11293.
Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. PMID: 34667539; PMCID: PMC8447925.
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PubMed Mentions:
14
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Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge. J Comput Aided Mol Des. 2021 07; 35(7):771-802.
Bergazin TD, Tielker N, Zhang Y, Mao J, Gunner MR, Francisco K, Ballatore C, Kast SM, Mobley DL. PMID: 34169394; PMCID: PMC8224998.
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PubMed Mentions:
16 Fields:
Translation:
Humans
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Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. J Phys Chem B. 2021 05 06; 125(17):4241-4261.
Baumann HM, Gapsys V, de Groot BL, Mobley DL. PMID: 33905257; PMCID: PMC8240641.
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PubMed Mentions:
18 Fields:
Translation:
Cells
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A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. J Chem Inf Model. 2021 03 22; 61(3):1048-1052.
Ge Y, Hahn DF, Mobley DL. PMID: 33686853; PMCID: PMC8208087.
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PubMed Mentions:
8 Fields:
-
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. J Comput Aided Mol Des. 2021 03; 35(3):271-284.
Ehrman JN, Lim VT, Bannan CC, Thi N, Kyu DY, Mobley DL. PMID: 33506360; PMCID: PMC8162916.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J Comput Aided Mol Des. 2021 01; 35(1):1-35.
Amezcua M, El Khoury L, Mobley DL. PMID: 33392951; PMCID: PMC8121194.
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PubMed Mentions:
26 Fields:
Translation:
HumansCells
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Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. J Comput Aided Mol Des. 2021 02; 35(2):131-166.
Isik M, Rustenburg AS, Rizzi A, Gunner MR, Mobley DL, Chodera JD. PMID: 33394238; PMCID: PMC7904668.
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PubMed Mentions:
10 Fields:
Translation:
Cells
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Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target. ACS Infect Dis. 2021 01 08; 7(1):174-188.
Burley KH, Cuthbert BJ, Basu P, Newcombe J, Irimpan EM, Quechol R, Foik IP, Mobley DL, Beste DJV, Goulding CW. PMID: 33356117; PMCID: PMC8083904.
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PubMed Mentions:
1 Fields:
Translation:
HumansCells
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Reversibly Sampling Conformations and Binding Modes Using Molecular Darting. J Chem Theory Comput. 2021 Jan 12; 17(1):302-314.
Gill SC, Mobley DL. PMID: 33289558; PMCID: PMC8121195.
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PubMed Mentions:
2 Fields:
Translation:
Cells
-
Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res. 2020; 9.
Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. PMID: 33604023; PMCID: PMC7863993.
View in:
PubMed Mentions:
18 Fields:
Translation:
Cells
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Kinetics and free energy of ligand dissociation using weighted ensemble milestoning. J Chem Phys. 2020 Oct 21; 153(15):154117.
Ray D, Gokey T, Mobley DL, Andricioaei I. PMID: 33092382.
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PubMed Mentions:
4 Fields:
-
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des. 2021 02; 35(2):167-177.
Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. PMID: 32968887; PMCID: PMC7904576.
View in:
PubMed Mentions:
12 Fields:
Translation:
Cells
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Implementation of a Hospital-Wide Protocol Reduces Time to Decompression and Length of Stay in Patients with Stone-Related Obstructive Pyelonephritis with Sepsis. J Endourol. 2021 01; 35(1):77-83.
Haas CR, Smigelski M, Sebesta EM, Mobley D, Shah O. PMID: 32668984.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations. Sci Rep. 2020 08 12; 10(1):13587.
Lim VT, Geragotelis AD, Lim NM, Freites JA, Tombola F, Mobley DL, Tobias DJ. PMID: 32788614; PMCID: PMC7423955.
View in:
PubMed Mentions:
4 Fields:
Translation:
HumansCells
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Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Commun Chem. 2020; 3.
Schauperl M, Nerenberg PS, Jang H, Wang LP, Bayly CI, Mobley DL, Gilson MK. PMID: 34136662; PMCID: PMC8204736.
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PubMed Mentions:
25
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Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations. J Chem Theory Comput. 2020 Apr 14; 16(4):2778-2794.
Lim NM, Osato M, Warren GL, Mobley DL. PMID: 32167763; PMCID: PMC7325745.
View in:
PubMed Mentions:
6 Fields:
Translation:
Cells
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Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J Comput Aided Mol Des. 2020 04; 34(4):335-370.
Isik M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. PMID: 32107702; PMCID: PMC7138020.
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PubMed Mentions:
24 Fields:
Translation:
Cells
-
Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics. J Chem Theory Comput. 2020 Mar 10; 16(3):1854-1865.
Sasmal S, Gill SC, Lim NM, Mobley DL. PMID: 32058713; PMCID: PMC7325746.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansCells
-
An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat Methods. 2020 03; 17(3):311-318.
Nainar S, Cuthbert BJ, Lim NM, England WE, Ke K, Sophal K, Quechol R, Mobley DL, Goulding CW, Spitale RC. PMID: 32015544; PMCID: PMC8518020.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansAnimalsCells
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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des. 2020 05; 34(5):601-633.
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, Chodera JD. PMID: 31984465; PMCID: PMC7282318.
View in:
PubMed Mentions:
37 Fields:
Translation:
Cells
-
Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living J Comput Mol Sci. 2020; 2(1).
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. PMID: 34458687; PMCID: PMC8388617.
View in:
PubMed Mentions:
71
-
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J Comput Aided Mol Des. 2020 04; 34(4):405-420.
Isik M, Levorse D, Mobley DL, Rhodes T, Chodera JD. PMID: 31858363; PMCID: PMC7301889.
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PubMed Mentions:
28 Fields:
-
Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Struct Dyn. 2019 Nov; 6(6):064704.
Wych DC, Fraser JS, Mobley DL, Wall ME. PMID: 31867408; PMCID: PMC6920053.
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PubMed Mentions:
5
-
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. J Comput Aided Mol Des. 2020 02; 34(2):163-177.
Sasmal S, El Khoury L, Mobley DL. PMID: 31781990; PMCID: PMC8208075.
View in:
PubMed Mentions:
6 Fields:
Translation:
HumansCells
-
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. J Comput Chem. 2020 01 30; 41(3):247-257.
Yang Q, Burchett W, Steeno GS, Liu S, Yang M, Mobley DL, Hou X. PMID: 31721260; PMCID: PMC6917845.
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PubMed Mentions:
14 Fields:
-
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. J Comput Aided Mol Des. 2019 12; 33(12):1011-1020.
El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL. PMID: 31691919; PMCID: PMC7027993.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansCells
-
Structure of a Mycobacterium tuberculosis Heme-Degrading Protein, MhuD, Variant in Complex with Its Product. Biochemistry. 2019 11 19; 58(46):4610-4620.
Chao A, Burley KH, Sieminski PJ, de Miranda R, Chen X, Mobley DL, Goulding CW. PMID: 31638374; PMCID: PMC7045704.
View in:
PubMed Mentions:
3 Fields:
Translation:
HumansCells
-
Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. J Chem Theory Comput. 2019 Nov 12; 15(11):6225-6242.
Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson MK. PMID: 31603667; PMCID: PMC7328435.
View in:
PubMed Mentions:
13 Fields:
-
Binding Modes and Metabolism of Caffeine. Chem Res Toxicol. 2019 07 15; 32(7):1374-1383.
Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C. PMID: 31132250; PMCID: PMC6635882.
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PubMed Mentions:
5 Fields:
Translation:
HumansCells
-
Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development. J Chem Theory Comput. 2019 May 14; 15(5):3066-3074.
Duarte Ramos Matos G, Calabrò G, Mobley DL. PMID: 30939010; PMCID: PMC6663494.
View in:
PubMed Mentions:
3 Fields:
-
Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome. Nucleic Acids Res. 2019 04 08; 47(6):3223-3232.
Pellegrino S, Meyer M, Könst ZA, Holm M, Voora VK, Kashinskaya D, Zanette C, Mobley DL, Yusupova G, Vanderwal CD, Blanchard SC, Yusupov M. PMID: 30759226; PMCID: PMC6451132.
View in:
PubMed Mentions:
10 Fields:
Translation:
HumansAnimalsCells
-
Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. J Am Chem Soc. 2019 03 20; 141(11):4711-4720.
Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. PMID: 30834751; PMCID: PMC6438627.
View in:
PubMed Mentions:
17 Fields:
Translation:
Cells
-
Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. J Chem Inf Model. 2019 05 28; 59(5):1957-1964.
Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL. PMID: 30742770; PMCID: PMC6538459.
View in:
PubMed Mentions:
6 Fields:
Translation:
Cells
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Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo. J Chem Theory Comput. 2019 Mar 12; 15(3):1848-1862.
Burley KH, Gill SC, Lim NM, Mobley DL. PMID: 30677291; PMCID: PMC6537864.
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PubMed Mentions:
10 Fields:
-
Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput. 2019 Jan 08; 15(1):402-423.
Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. PMID: 30512951; PMCID: PMC6467725.
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PubMed Mentions:
16 Fields:
Translation:
HumansCells
-
Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living J Comput Mol Sci. 2019; 1(1).
Braun E, Gilmer J, Mayes HB, Mobley DL, Monroe JI, Prasad S, Zuckerman DM. PMID: 31788666; PMCID: PMC6884151.
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PubMed Mentions:
37
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Efficacy and safety of partial splenic embolization for hypersplenism in pre- and post-liver transplant patients: A 16-year comparative analysis. Clin Imaging. 2019 Mar - Apr; 54:71-77.
DuBois B, Mobley D, Chick JFB, Srinivasa RN, Wilcox C, Weintraub J. PMID: 30553121.
View in:
PubMed Mentions:
4 Fields:
Translation:
Humans
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Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des. 2018 10; 32(10):937-963.
Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. PMID: 30415285; PMCID: PMC6301044.
View in:
PubMed Mentions:
58 Fields:
Translation:
Cells
-
pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J Comput Aided Mol Des. 2018 10; 32(10):1117-1138.
Isik M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD. PMID: 30406372; PMCID: PMC6367941.
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PubMed Mentions:
23 Fields:
-
Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov 13; 14(11):6076-6092.
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. PMID: 30351006; PMCID: PMC6245550.
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PubMed Mentions:
60 Fields:
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Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. J Chem Theory Comput. 2018 Nov 13; 14(11):5567-5582.
Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. PMID: 30289712.
View in:
PubMed Mentions:
33 Fields:
-
SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model. J Comput Aided Mol Des. 2018 10; 32(10):1165-1177.
Bannan CC, Mobley DL, Skillman AG. PMID: 30324305; PMCID: PMC6438616.
View in:
PubMed Mentions:
9 Fields:
Translation:
Cells
-
Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. J Chem Inf Model. 2018 09 24; 58(9):1779-1797.
Riquelme M, Lara A, Mobley DL, Verstraelen T, Matamala AR, Vöhringer-Martinez E. PMID: 30125107; PMCID: PMC6195221.
View in:
PubMed Mentions:
10 Fields:
-
Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000Res. 2018; 7:686.
Duarte Ramos Matos G, Mobley DL. PMID: 30109026; PMCID: PMC6069752.
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PubMed Mentions:
1 Fields:
-
Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. J Membr Biol. 2018 06; 251(3):379-391.
Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS. PMID: 29550876; PMCID: PMC6030514.
View in:
PubMed Mentions:
11 Fields:
Translation:
Cells
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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. J Phys Chem B. 2018 05 31; 122(21):5579-5598.
Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. PMID: 29486559; PMCID: PMC5980761.
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PubMed Mentions:
27 Fields:
Translation:
Cells
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Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations. J Chem Theory Comput. 2018 Feb 13; 14(2):759-767.
Yang X, Lei H, Gao P, Thomas DG, Mobley DL, Baker NA. PMID: 29293342; PMCID: PMC6906122.
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PubMed Mentions:
5 Fields:
Translation:
Cells
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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem. 2017 12 19; 10(1):8-16.
Cremer PS, Flood AH, Gibb BC, Mobley DL. PMID: 29256514.
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PubMed Mentions:
30 Fields:
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Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 08; 31(8):777.
Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 28752343.
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PubMed Mentions: Fields:
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Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Nat Chem. 2017 11; 9(11):1140-1149.
Könst ZA, Szklarski AR, Pellegrino S, Michalak SE, Meyer M, Zanette C, Cencic R, Nam S, Voora VK, Horne DA, Pelletier J, Mobley DL, Yusupova G, Yusupov M, Vanderwal CD. PMID: 29064494; PMCID: PMC6021127.
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PubMed Mentions:
11 Fields:
Translation:
HumansAnimalsCells
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Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. J Chem Eng Data. 2017 May 11; 62(5):1559-1569.
Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. PMID: 29056756; PMCID: PMC5648357.
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PubMed Mentions:
43
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Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 05 22; 46:531-558.
Mobley DL, Gilson MK. PMID: 28399632; PMCID: PMC5544526.
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PubMed Mentions:
116 Fields:
Translation:
Cells
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Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies. J Phys Chem B. 2017 04 20; 121(15):3458-3472.
Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA. PMID: 27966363; PMCID: PMC5398953.
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PubMed Mentions:
3 Fields:
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A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Curr Top Med Chem. 2017; 17(23):2577-2585.
Abel R, Wang L, Mobley DL, Friesner RA. PMID: 28413950.
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PubMed Mentions:
36 Fields:
Translation:
Cells
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Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations. Phys Chem Chem Phys. 2016 Nov 30; 18(47):32358-32368.
Evoli S, Mobley DL, Guzzi R, Rizzuti B. PMID: 27854368; PMCID: PMC5130592.
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PubMed Mentions:
24 Fields:
Translation:
HumansCells
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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 01; 31(1):147-161.
Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 27787702; PMCID: PMC5581938.
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PubMed Mentions:
71 Fields:
Translation:
Cells
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Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):945-958.
Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD. PMID: 27718028; PMCID: PMC5209288.
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PubMed Mentions:
31 Fields:
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Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):927-944.
Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. PMID: 27677750; PMCID: PMC5209301.
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PubMed Mentions:
59 Fields:
Translation:
Cells
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Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 01; 31(1):1-19.
Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. PMID: 27658802; PMCID: PMC5241188.
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PubMed Mentions:
79 Fields:
Translation:
Cells
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Sensitivity in Binding Free Energies Due to Protein Reorganization. J Chem Theory Comput. 2016 Sep 13; 12(9):4620-31.
Lim NM, Wang L, Abel R, Mobley DL. PMID: 27462935; PMCID: PMC5021633.
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PubMed Mentions:
31 Fields:
Translation:
Cells
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Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water. J Chem Theory Comput. 2016 Aug 09; 12(8):4015-24.
Bannan CC, Calabró G, Kyu DY, Mobley DL. PMID: 27434695; PMCID: PMC5053177.
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PubMed Mentions:
54 Fields:
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Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput. 2016 Apr 12; 12(4):1930-41.
Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. PMID: 26878198; PMCID: PMC4945102.
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PubMed Mentions:
14 Fields:
Translation:
Cells
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A Python tool to set up relative free energy calculations in GROMACS. J Comput Aided Mol Des. 2015 Nov; 29(11):1007-14.
Klimovich PV, Mobley DL. PMID: 26487189; PMCID: PMC4749424.
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PubMed Mentions:
12 Fields:
Translation:
Cells
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Is ring breaking feasible in relative binding free energy calculations? J Chem Inf Model. 2015 Apr 27; 55(4):727-35.
Liu S, Wang L, Mobley DL. PMID: 25835054; PMCID: PMC4489933.
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PubMed Mentions:
22 Fields:
Translation:
HumansCells
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Guidelines for the analysis of free energy calculations. J Comput Aided Mol Des. 2015 May; 29(5):397-411.
Klimovich PV, Shirts MR, Mobley DL. PMID: 25808134; PMCID: PMC4420631.
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PubMed Mentions:
133 Fields:
Translation:
Cells
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Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. J Chem Theory Comput. 2015 Mar 10; 11(3):1347.
Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 26579779; PMCID: PMC4675652.
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PubMed Mentions:
6 Fields:
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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. J Am Chem Soc. 2015 Feb 25; 137(7):2695-703.
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, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. PMID: 25625324.
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PubMed Mentions:
404 Fields:
Translation:
Cells
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Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation. J Chem Phys. 2015 Jan 28; 142(4):044508.
Paluch AS, Parameswaran S, Liu S, Kolavennu A, Mobley DL. PMID: 25637996; PMCID: PMC4312346.
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PubMed Mentions:
11 Fields:
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Box size effects are negligible for solvation free energies of neutral solutes. J Comput Aided Mol Des. 2014 Aug; 28(8):825-9.
Parameswaran S, Mobley DL. PMID: 24976043.
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PubMed Mentions:
11 Fields:
Translation:
Cells
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FreeSolv: a database of experimental and calculated hydration free energies, with input files. J Comput Aided Mol Des. 2014 Jul; 28(7):711-20.
Mobley DL, Guthrie JP. PMID: 24928188; PMCID: PMC4113415.
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PubMed Mentions:
99 Fields:
Translation:
Cells
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A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. J Phys Chem B. 2014 Jun 19; 118(24):6438-46.
Fennell CJ, Wymer KL, Mobley DL. PMID: 24702668; PMCID: PMC4064691.
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PubMed Mentions:
24 Fields:
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Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Mar; 28(3):135-50.
Mobley DL, Wymer KL, Lim NM, Guthrie JP. PMID: 24615156; PMCID: PMC4006301.
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PubMed Mentions:
81 Fields:
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The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17.
Muddana HS, Fenley AT, Mobley DL, Gilson MK. PMID: 24599514; PMCID: PMC4053502.
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PubMed Mentions:
96 Fields:
Translation:
Cells
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Blind prediction of HIV integrase binding from the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Apr; 28(4):327-45.
Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. PMID: 24595873; PMCID: PMC4331050.
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PubMed Mentions:
36 Fields:
Translation:
HumansCells
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Interrogating HIV integrase for compounds that bind--a SAMPL challenge. J Comput Aided Mol Des. 2014 Apr; 28(4):347-62.
Peat TS, Dolezal O, Newman J, Mobley D, Deadman JJ. PMID: 24532034; PMCID: PMC4346355.
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PubMed Mentions:
18 Fields:
Translation:
HumansCells
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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. J Chem Phys. 2013 Nov 14; 139(18):184103.
Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. PMID: 24320250; PMCID: PMC3838431.
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PubMed Mentions:
83 Fields:
Translation:
AnimalsCells
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Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration. J Med Chem. 2013 Nov 14; 56(21):8543-60.
Zheng YC, Duan YC, Ma JL, Xu RM, Zi X, Lv WL, Wang MM, Ye XW, Zhu S, Mobley D, Zhu YY, Wang JW, Li JF, Wang ZR, Zhao W, Liu HM. PMID: 24131029; PMCID: PMC3881423.
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PubMed Mentions:
61 Fields:
Translation:
HumansAnimalsCells
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Lead optimization mapper: automating free energy calculations for lead optimization. J Comput Aided Mol Des. 2013 Sep; 27(9):755-70.
Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. PMID: 24072356; PMCID: PMC3837551.
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PubMed Mentions:
48 Fields:
Translation:
HumansCells
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Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83.
Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. PMID: 23896298; PMCID: PMC3962782.
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PubMed Mentions:
25 Fields:
Translation:
Cells
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Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput. 2013 Jul 09; 9(7):3072-3083.
Rocklin GJ, Mobley DL, Dill KA. PMID: 24015114; PMCID: PMC3763860.
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PubMed Mentions:
10 Fields:
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3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters. Bioorg Med Chem Lett. 2013 Aug 01; 23(15):4404-7.
Thaxton A, Izenwasser S, Wade D, Stevens ED, Mobley DL, Jaber V, Lomenzo SA, Trudell ML. PMID: 23806554; PMCID: PMC3733996.
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PubMed Mentions: Fields:
Translation:
Cells
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Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys. 2013 Feb 28; 138(8):085104.
Rocklin GJ, Mobley DL, Dill KA. PMID: 23464180; PMCID: PMC3598757.
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PubMed Mentions:
16 Fields:
Translation:
Cells
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An introduction to best practices in free energy calculations. Methods Mol Biol. 2013; 924:271-311.
Shirts MR, Mobley DL. PMID: 23034753.
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PubMed Mentions:
24 Fields:
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Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu Rev Biophys. 2013; 42:121-42.
Chodera JD, Mobley DL. PMID: 23654303; PMCID: PMC4124006.
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PubMed Mentions:
148 Fields:
Translation:
Cells
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Perspective: Alchemical free energy calculations for drug discovery. J Chem Phys. 2012 Dec 21; 137(23):230901.
Mobley DL, Klimovich PV. PMID: 23267463; PMCID: PMC3537745.
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PubMed Mentions:
82 Fields:
Translation:
Cells
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Alchemical prediction of hydration free energies for SAMPL. J Comput Aided Mol Des. 2012 May; 26(5):551-62.
Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. PMID: 22198475; PMCID: PMC3583515.
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PubMed Mentions:
31 Fields:
Translation:
Cells
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Let's get honest about sampling. J Comput Aided Mol Des. 2012 Jan; 26(1):93-5.
Mobley DL. PMID: 22113833.
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PubMed Mentions:
46 Fields:
Translation:
HumansCells
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Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation. J Chem Theory Comput. 2011 Sep 13; 7(9):2910-8.
Paluch AS, Mobley DL, Maginn EJ. PMID: 26605480.
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PubMed Mentions:
7 Fields:
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Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011 Apr; 21(2):150-60.
Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. PMID: 21349700; PMCID: PMC3085996.
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PubMed Mentions:
215 Fields:
Translation:
Cells
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Synthesis and structure-activity studies of benzyl ester meperidine and normeperidine derivatives as selective serotonin transporter ligands. Bioorg Med Chem. 2010 Dec 01; 18(23):8356-64.
Gu X, Izenwasser S, Wade D, Housman A, Gulasey G, Rhoden JB, Savoie CD, Mobley DL, Lomenzo SA, Trudell ML. PMID: 20980153; PMCID: PMC3713777.
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PubMed Mentions: Fields:
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Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J Comput Aided Mol Des. 2010 Apr; 24(4):307-16.
Klimovich PV, Mobley DL. PMID: 20372973.
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PubMed Mentions:
50 Fields:
Translation:
Cells
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Current status of the AMOEBA polarizable force field. J Phys Chem B. 2010 Mar 04; 114(8):2549-64.
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. PMID: 20136072; PMCID: PMC2918242.
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PubMed Mentions:
335 Fields:
Translation:
Cells
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Synthesis and monoamine transporter affinity of 3alpha-arylmethoxy-3beta-arylnortropanes. Bioorg Med Chem Lett. 2009 Dec 15; 19(24):6865-8.
Kaur H, Izenwasser S, Verma A, Wade D, Housman A, Stevens ED, Mobley DL, Trudell ML. PMID: 19896846; PMCID: PMC2788963.
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PubMed Mentions:
2 Fields:
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Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol. 2009 Dec 11; 394(4):747-63.
Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. PMID: 19782087; PMCID: PMC2788029.
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PubMed Mentions:
84 Fields:
Translation:
Cells
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Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 08; 5(9):2486-2502.
McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. PMID: 20161451; PMCID: PMC2790287.
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PubMed Mentions:
103 Fields:
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Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure. 2009 Apr 15; 17(4):489-98.
Mobley DL, Dill KA. PMID: 19368882; PMCID: PMC2756098.
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PubMed Mentions:
223 Fields:
Translation:
Cells
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Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B. 2009 Apr 09; 113(14):4533-7.
Mobley DL, Bayly CI, Cooper MD, Dill KA. PMID: 19271713; PMCID: PMC2684682.
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PubMed Mentions:
35 Fields:
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Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput. 2009 Feb 10; 5(2):350-358.
Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 20150953; PMCID: PMC2701304.
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PubMed Mentions:
128 Fields:
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Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14.
Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. PMID: 18251538; PMCID: PMC2745216.
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PubMed Mentions:
41 Fields:
Translation:
Cells
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Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem. 2008 Feb 28; 51(4):769-79.
Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. PMID: 18215013.
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PubMed Mentions:
121 Fields:
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Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B. 2008 Jan 24; 112(3):938-46.
Mobley DL, Dill KA, Chodera JD. PMID: 18171044; PMCID: PMC2745223.
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PubMed Mentions:
47 Fields:
Translation:
Cells
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Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys. 2007 Dec 07; 127(21):214108.
Steinbrecher T, Mobley DL, Case DA. PMID: 18067350.
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PubMed Mentions:
101 Fields:
Translation:
Cells
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Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B. 2007 Nov 15; 111(45):13052-63.
Shirts MR, Mobley DL, Chodera JD, Pande VS. PMID: 17949030.
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PubMed Mentions:
80 Fields:
Translation:
Cells
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Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34.
Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. PMID: 17599350; PMCID: PMC2104542.
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PubMed Mentions:
130 Fields:
Translation:
Cells
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Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B. 2007 Mar 08; 111(9):2242-54.
Mobley DL, Dumont E, Chodera JD, Dill KA. PMID: 17291029.
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PubMed Mentions:
99 Fields:
Translation:
Cells
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The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput. 2007; 3(4):1231-1235.
Mobley DL, Chodera JD, Dill KA. PMID: 18843379; PMCID: PMC2562444.
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PubMed Mentions:
86 Fields:
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A mathematical model of glioblastoma tumor spheroid invasion in a three-dimensional in vitro experiment. Biophys J. 2007 Jan 01; 92(1):356-65.
Stein AM, Demuth T, Mobley D, Berens M, Sander LM. PMID: 17040992; PMCID: PMC1697862.
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PubMed Mentions:
91 Fields:
Translation:
HumansCells
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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys. 2006 Aug 28; 125(8):084902.
Mobley DL, Chodera JD, Dill KA. PMID: 16965052; PMCID: PMC3583553.
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PubMed Mentions:
118 Fields:
Translation:
Cells
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Treatment of a biliary-venous fistula following percutaneous biopsy in a pediatric living related liver transplant patient. Pediatr Radiol. 2006 Jun; 36(6):555-7.
Weintraub JL, Hawari A, English B, Mobley D. PMID: 16596368.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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Modeling amyloid beta-peptide insertion into lipid bilayers. Biophys J. 2004 Jun; 86(6):3585-97.
Mobley DL, Cox DL, Singh RR, Maddox MW, Longo ML. PMID: 15189856; PMCID: PMC1304261.
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PubMed Mentions:
21 Fields:
Translation:
HumansCells
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Simulations of oligomeric intermediates in prion diseases. Biophys J. 2003 Oct; 85(4):2213-23.
Mobley DL, Cox DL, Singh RR, Kulkarni RV, Slepoy A. PMID: 14507687; PMCID: PMC1303448.
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PubMed Mentions:
2 Fields:
Translation:
HumansAnimalsCells