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Items: 1 to 50 of 133

1.

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL.

Nat Commun. 2018 Aug 6;9(1):3085. doi: 10.1038/s41467-018-05406-y.

2.

Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Yin J, Henriksen NM, Muddana HS, Gilson MK.

J Chem Theory Comput. 2018 Jul 10;14(7):3621-3632. doi: 10.1021/acs.jctc.8b00318. Epub 2018 Jun 22.

PMID:
29874074
3.

Motor-like Properties of Nonmotor Enzymes.

Slochower DR, Gilson MK.

Biophys J. 2018 May 8;114(9):2174-2179. doi: 10.1016/j.bpj.2018.02.008.

PMID:
29742410
4.

Substrate-driven chemotactic assembly in an enzyme cascade.

Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A.

Nat Chem. 2018 Mar;10(3):311-317. doi: 10.1038/nchem.2905. Epub 2017 Dec 18.

PMID:
29461522
5.

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

Kantonen SA, Henriksen NM, Gilson MK.

Biochim Biophys Acta. 2018 Mar;1862(3):692-704. doi: 10.1016/j.bbagen.2017.11.020. Epub 2017 Dec 6.

PMID:
29221984
6.

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE.

J Comput Aided Mol Des. 2018 Jan;32(1):1-20. doi: 10.1007/s10822-017-0088-4. Epub 2017 Dec 4.

PMID:
29204945
7.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T.

J Chem Theory Comput. 2018 Jan 9;14(1):418-425. doi: 10.1021/acs.jctc.7b00592. Epub 2017 Dec 8.

PMID:
29161510
8.

HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM.

J Phys Chem B. 2017 Dec 14;121(49):11144-11162. doi: 10.1021/acs.jpcb.7b09175. Epub 2017 Dec 1.

PMID:
29140701
9.

Testing inhomogeneous solvation theory in structure-based ligand discovery.

Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6839-E6846. doi: 10.1073/pnas.1703287114. Epub 2017 Jul 31.

10.

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. No abstract available.

11.

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.

Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Sep 12;13(9):4253-4269. doi: 10.1021/acs.jctc.7b00359. Epub 2017 Aug 4.

12.

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain.

Heinzelmann G, Henriksen NM, Gilson MK.

J Chem Theory Comput. 2017 Jul 11;13(7):3260-3275. doi: 10.1021/acs.jctc.7b00275. Epub 2017 Jun 13.

13.

Attractive Interactions between Heteroallenes and the Cucurbituril Portal.

Reany O, Li A, Yefet M, Gilson MK, Keinan E.

J Am Chem Soc. 2017 Jun 21;139(24):8138-8145. doi: 10.1021/jacs.6b13005. Epub 2017 Jun 7.

14.

Predicting Binding Free Energies: Frontiers and Benchmarks.

Mobley DL, Gilson MK.

Annu Rev Biophys. 2017 May 22;46:531-558. doi: 10.1146/annurev-biophys-070816-033654. Epub 2017 Apr 7. Review.

15.

Bio-inspired CO2 reduction by a rhenium tricarbonyl bipyridine-based catalyst appended to amino acids and peptidic platforms: incorporating proton relays and hydrogen-bonding functional groups.

Chabolla SA, Machan CW, Yin J, Dellamary EA, Sahu S, Gianneschi NC, Gilson MK, Tezcan FA, Kubiak CP.

Faraday Discuss. 2017 Jun 2;198:279-300. doi: 10.1039/c7fd00003k.

16.

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase.

Lee KS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD.

Arch Biochem Biophys. 2017 Jan 1;613:1-11. doi: 10.1016/j.abb.2016.10.017. Epub 2016 Oct 29.

17.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED.

J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. Erratum in: J Comput Aided Mol Des. 2017 Jul 27;:.

18.

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB Jr, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK.

J Comput Aided Mol Des. 2016 Sep;30(9):651-668. Epub 2016 Sep 30.

19.

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL.

J Comput Aided Mol Des. 2016 Nov;30(11):927-944. doi: 10.1007/s10822-016-9954-8. Epub 2016 Sep 27.

20.

Overview of the SAMPL5 host-guest challenge: Are we doing better?

Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. Review.

21.

The SAMPL5 host-guest challenge: computing binding free energies andĀ enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

Yin J, Henriksen NM, Slochower DR, Gilson MK.

J Comput Aided Mol Des. 2017 Jan;31(1):133-145. doi: 10.1007/s10822-016-9970-8. Epub 2016 Sep 16.

22.

Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry.

Kantonen SA, Henriksen NM, Gilson MK.

Biochim Biophys Acta. 2017 Feb;1861(2):485-498. doi: 10.1016/j.bbagen.2016.09.002. Epub 2016 Sep 15.

23.

Erratum: "The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling" [J. Chem. Phys. 138, 224504 (2013)].

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Chem Phys. 2016 Jul 28;145(4):049902. doi: 10.1063/1.4960037. No abstract available.

PMID:
27475401
24.

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T.

J Comput Chem. 2016 Aug 5;37(21):2029-37. doi: 10.1002/jcc.24417. Epub 2016 Jun 18.

25.

Improving the Efficiency and Activity of Electrocatalysts for the Reduction of CO2 through Supramolecular Assembly with Amino Acid-Modified Ligands.

Machan CW, Yin J, Chabolla SA, Gilson MK, Kubiak CP.

J Am Chem Soc. 2016 Jul 6;138(26):8184-93. doi: 10.1021/jacs.6b03774. Epub 2016 Jun 23.

PMID:
27258781
26.

Evaluation of Representations and Response Models for Polarizable Force Fields.

Li A, Voronin A, Fenley AT, Gilson MK.

J Phys Chem B. 2016 Aug 25;120(33):8668-84. doi: 10.1021/acs.jpcb.6b03392. Epub 2016 Jun 16.

27.

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T.

J Phys Chem B. 2016 Sep 1;120(34):8743-56. doi: 10.1021/acs.jpcb.6b01094. Epub 2016 Jun 2.

28.

Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.

Nguyen CN, Kurtzman T, Gilson MK.

J Chem Theory Comput. 2016 Jan 12;12(1):414-29. doi: 10.1021/acs.jctc.5b00939. Epub 2015 Dec 4.

29.

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK.

J Chem Theory Comput. 2015 Oct 13;11(10):4555-64. doi: 10.1021/acs.jctc.5b00676. Epub 2015 Sep 18.

30.

Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.

Henriksen NM, Fenley AT, Gilson MK.

J Chem Theory Comput. 2015 Sep 8;11(9):4377-94.

31.

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1045-53. doi: 10.1093/nar/gkv1072. Epub 2015 Oct 19.

32.

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Nicola G, Berthold MR, Hedrick MP, Gilson MK.

Database (Oxford). 2015 Sep 16;2015. pii: bav087. doi: 10.1093/database/bav087. Print 2015.

33.

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM.

J Mol Recognit. 2016 Jan;29(1):10-21. doi: 10.1002/jmr.2489. Epub 2015 Aug 10.

34.

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.

Yin J, Fenley AT, Henriksen NM, Gilson MK.

J Phys Chem B. 2015 Aug 13;119(32):10145-55. doi: 10.1021/acs.jpcb.5b04262. Epub 2015 Aug 5.

35.

Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

Fenley AT, Muddana HS, Gilson MK.

PLoS One. 2014 Dec 11;9(12):e113119. doi: 10.1371/journal.pone.0113119. eCollection 2014.

36.

Dynamic architecture of a protein kinase.

McClendon CL, Kornev AP, Gilson MK, Taylor SS.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):E4623-31. doi: 10.1073/pnas.1418402111. Epub 2014 Oct 15. Erratum in: Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16973.

37.

Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity.

Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC.

J Am Chem Soc. 2014 Oct 29;136(43):15422-37. doi: 10.1021/ja5088216. Epub 2014 Oct 14.

38.

Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re(I) bipyridine catalysts at a lower overpotential.

Machan CW, Chabolla SA, Yin J, Gilson MK, Tezcan FA, Kubiak CP.

J Am Chem Soc. 2014 Oct 15;136(41):14598-607. doi: 10.1021/ja5085282. Epub 2014 Oct 6.

PMID:
25226161
39.

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies.

Fenley AT, Henriksen NM, Muddana HS, Gilson MK.

J Chem Theory Comput. 2014 Sep 9;10(9):4069-4078. Epub 2014 Jul 23.

40.

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.

Nguyen CN, Cruz A, Gilson MK, Kurtzman T.

J Chem Theory Comput. 2014 Jul 8;10(7):2769-2780. Epub 2014 Apr 3.

41.

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches.

Li A, Muddana HS, Gilson MK.

J Chem Theory Comput. 2014 Apr 8;10(4):1563-1575. Epub 2014 Feb 25.

42.

Correlation as a determinant of configurational entropy in supramolecular and protein systems.

Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson MK.

J Phys Chem B. 2014 Jun 19;118(24):6447-55. doi: 10.1021/jp411588b. Epub 2014 Apr 18.

43.

The SAMPL4 host-guest blind prediction challenge: an overview.

Muddana HS, Fenley AT, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2014 Apr;28(4):305-17. doi: 10.1007/s10822-014-9735-1. Epub 2014 Mar 6. Review.

44.

Digital chemistry in the Journal of Medicinal Chemistry.

Gilson MK, Georg G, Wang S.

J Med Chem. 2014 Feb 27;57(4):1137. doi: 10.1021/jm5002056. Epub 2014 Feb 12. No abstract available.

PMID:
24521446
45.

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method.

Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK.

J Comput Aided Mol Des. 2014 Apr;28(4):463-74. doi: 10.1007/s10822-014-9726-2. Epub 2014 Feb 8.

46.

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations.

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Comput Aided Mol Des. 2014 Mar;28(3):277-87. doi: 10.1007/s10822-014-9714-6. Epub 2014 Jan 30.

47.

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.

Velez-Vega C, Gilson MK.

J Comput Chem. 2013 Oct 15;34(27):2360-71. doi: 10.1002/jcc.23398. Epub 2013 Aug 26.

48.

The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Chem Phys. 2013 Jun 14;138(22):224504. doi: 10.1063/1.4808376.

49.

Charge Optimization Theory for Induced-Fit Ligands.

Shen Y, Gilson MK, Tidor B.

J Chem Theory Comput. 2012 Nov 13;8(11):4580-4592. Epub 2012 Jun 17.

50.

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding.

Fenley AT, Muddana HS, Gilson MK.

Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):20006-11. doi: 10.1073/pnas.1213180109. Epub 2012 Nov 13.

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