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Items: 1 to 20 of 70

1.

The dynamic conformational landscape of the protein methyltransferase SETD8.

Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M.

Elife. 2019 May 13;8. pii: e45403. doi: 10.7554/eLife.45403. [Epub ahead of print]

2.

What Makes a Kinase Promiscuous for Inhibitors?

Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA.

Cell Chem Biol. 2019 Mar 21;26(3):390-399.e5. doi: 10.1016/j.chembiol.2018.11.005. Epub 2019 Jan 3.

PMID:
30612951
3.

Toward Learned Chemical Perception of Force Field Typing Rules.

Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL.

J Chem Theory Comput. 2019 Jan 8;15(1):402-423. doi: 10.1021/acs.jctc.8b00821. Epub 2018 Dec 24.

PMID:
30512951
4.

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10.

PMID:
30415285
5.

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):1117-1138. doi: 10.1007/s10822-018-0168-0. Epub 2018 Nov 7.

PMID:
30406372
6.

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.

7.

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes.

Swenson DWH, Prinz JH, Noe F, Chodera JD, Bolhuis PG.

J Chem Theory Comput. 2019 Feb 12;15(2):837-856. doi: 10.1021/acs.jctc.8b00627. Epub 2018 Dec 31.

8.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.

PMID:
30351006
9.

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.

Swenson DWH, Prinz JH, Noe F, Chodera JD, Bolhuis PG.

J Chem Theory Comput. 2019 Feb 12;15(2):813-836. doi: 10.1021/acs.jctc.8b00626. Epub 2018 Dec 31.

10.

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics.

Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL.

PLoS One. 2018 Sep 13;13(9):e0203224. doi: 10.1371/journal.pone.0203224. eCollection 2018.

11.

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations.

Hauser K, Negron C, Albanese SK, Ray S, Steinbrecher T, Abel R, Chodera JD, Wang L.

Commun Biol. 2018;1. pii: 70. doi: 10.1101/239012. Epub 2018 Jun 13.

12.

An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression.

Albanese SK, Parton DL, Işık M, Rodríguez-Laureano L, Hanson SM, Behr JM, Gradia S, Jeans C, Levinson NM, Seeliger MA, Chodera JD.

Biochemistry. 2018 Aug 7;57(31):4675-4689. doi: 10.1021/acs.biochem.7b01081. Epub 2018 Jul 26.

PMID:
30004690
13.

Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations.

Intlekofer AM, Shih AH, Wang B, Nazir A, Rustenburg AS, Albanese SK, Patel M, Famulare C, Correa FM, Takemoto N, Durani V, Liu H, Taylor J, Farnoud N, Papaemmanuil E, Cross JR, Tallman MS, Arcila ME, Roshal M, Petsko GA, Wu B, Choe S, Konteatis ZD, Biller SA, Chodera JD, Thompson CB, Levine RL, Stein EM.

Nature. 2018 Jul;559(7712):125-129. doi: 10.1038/s41586-018-0251-7. Epub 2018 Jun 27.

14.

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD.

J Phys Chem B. 2018 May 31;122(21):5466-5486. doi: 10.1021/acs.jpcb.7b11734.

PMID:
29649876
15.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL.

J Phys Chem B. 2018 May 31;122(21):5579-5598. doi: 10.1021/acs.jpcb.7b11820. Epub 2018 Mar 12.

16.

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.

Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM.

Elife. 2018 Feb 21;7. pii: e32766. doi: 10.7554/eLife.32766.

17.

Quantitative self-assembly prediction yields targeted nanomedicines.

Shamay Y, Shah J, Işık M, Mizrachi A, Leibold J, Tschaharganeh DF, Roxbury D, Budhathoki-Uprety J, Nawaly K, Sugarman JL, Baut E, Neiman MR, Dacek M, Ganesh KS, Johnson DC, Sridharan R, Chu KL, Rajasekhar VK, Lowe SW, Chodera JD, Heller DA.

Nat Mater. 2018 Apr;17(4):361-368. doi: 10.1038/s41563-017-0007-z. Epub 2018 Feb 5.

18.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL.

J Chem Eng Data. 2017 May 11;62(5):1559-1569. doi: 10.1021/acs.jced.7b00104. Epub 2017 Apr 24.

19.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS.

PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul.

20.

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH.

Intlekofer AM, Wang B, Liu H, Shah H, Carmona-Fontaine C, Rustenburg AS, Salah S, Gunner MR, Chodera JD, Cross JR, Thompson CB.

Nat Chem Biol. 2017 May;13(5):494-500. doi: 10.1038/nchembio.2307. Epub 2017 Mar 6.

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