Chodera JD - Search Results

1

Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.

Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Zhang I, et al. Among authors: chodera jd. J Chem Theory Comput. 2024 Jan 23;20(2):990-991. doi: 10.1021/acs.jctc.3c01298. Epub 2024 Jan 2. J Chem Theory Comput. 2024. PMID: 38164914 No abstract available.

2

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge.

Işık M, Levorse D, Mobley DL, Rhodes T, Chodera JD. Işık M, et al. Among authors: chodera jd. J Comput Aided Mol Des. 2020 Apr;34(4):405-420. doi: 10.1007/s10822-019-00271-3. Epub 2019 Dec 19. J Comput Aided Mol Des. 2020. PMID: 31858363 Free PMC article.

3

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].

Hahn DF, Bayly CI, Macdonald HEB, Chodera JD, Mey ASJS, Mobley DL, Benito LP, Schindler CEM, Tresadern G, Warren GL. Hahn DF, et al. Among authors: chodera jd. Living J Comput Mol Sci. 2022;4(1):1497. doi: 10.33011/livecoms.4.1.1497. Epub 2022 Aug 30. Living J Comput Mol Sci. 2022. PMID: 36382113 Free PMC article.

4

Crowdsourcing drug discovery for pandemics.

Chodera J, Lee AA, London N, von Delft F. Chodera J, et al. Nat Chem. 2020 Jul;12(7):581. doi: 10.1038/s41557-020-0496-2. Nat Chem. 2020. PMID: 32555379 No abstract available.

5

Uncertainty estimation.

Noé F, Chodera JD. Noé F, et al. Among authors: chodera jd. Adv Exp Med Biol. 2014;797:61-74. doi: 10.1007/978-94-007-7606-7_5. Adv Exp Med Biol. 2014. PMID: 24297275 No abstract available.

6

Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Chodera JD, Mobley DL. Chodera JD, et al. Annu Rev Biophys. 2013;42:121-42. doi: 10.1146/annurev-biophys-083012-130318. Annu Rev Biophys. 2013. PMID: 23654303 Free PMC article. Review.

7

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Chodera JD, et al. J Chem Phys. 2007 Apr 21;126(15):155101. doi: 10.1063/1.2714538. J Chem Phys. 2007. PMID: 17461665

8

Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model.

Morris A, McCorkindale W, Consortium TCM, Drayman N, Chodera JD, Tay S, London N, Lee AA. Morris A, et al. Among authors: chodera jd. Chem Commun (Camb). 2021 Jun 15;57(48):5909-5912. doi: 10.1039/d1cc00050k. Chem Commun (Camb). 2021. PMID: 34008627 Free PMC article.

9

Protein folding by zipping and assembly.

Ozkan SB, Wu GA, Chodera JD, Dill KA. Ozkan SB, et al. Among authors: chodera jd. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11987-92. doi: 10.1073/pnas.0703700104. Epub 2007 Jul 9. Proc Natl Acad Sci U S A. 2007. PMID: 17620603 Free PMC article.

10

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.

Lee TS, Chong LT, Chodera JD, Kollman PA. Lee TS, et al. Among authors: chodera jd. J Am Chem Soc. 2001 Dec 26;123(51):12837-48. doi: 10.1021/ja011096f. J Am Chem Soc. 2001. PMID: 11749542

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