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Items: 1 to 50 of 592

1.

A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics.

Aboelkassem Y, McCabe KJ, Huber GA, Regnier M, McCammon JA, McCulloch AD.

Biophys J. 2019 Aug 9. pii: S0006-3495(19)30670-8. doi: 10.1016/j.bpj.2019.08.003. [Epub ahead of print]

PMID:
31547973
2.

The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution.

Palermo G, Ricci CG, McCammon JA.

Phys Today. 2019 Apr;72(4):30-36. doi: 10.1063/PT.3.4182.

3.

The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation.

Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ.

ACM Trans Math Softw. 2019 Aug;45(3). pii: 28. doi: 10.1145/3321515.

PMID:
31474782
4.

Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins.

Sztain T, Bartholow TG, McCammon JA, Burkart MD.

Biochemistry. 2019 Aug 27;58(34):3557-3560. doi: 10.1021/acs.biochem.9b00612. Epub 2019 Aug 14.

PMID:
31397556
5.

Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics.

Zhou S, Weiß RG, Cheng LT, Dzubiella J, McCammon JA, Li B.

Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):14989-14994. doi: 10.1073/pnas.1902719116. Epub 2019 Jul 3.

PMID:
31270236
6.

Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein.

Sztain T, Patel A, Lee DJ, Davis TD, McCammon JA, Burkart MD.

Angew Chem Int Ed Engl. 2019 Aug 5;58(32):10888-10892. doi: 10.1002/anie.201903815. Epub 2019 Jul 2.

PMID:
31140212
7.

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.

Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G.

ACS Cent Sci. 2019 Apr 24;5(4):651-662. doi: 10.1021/acscentsci.9b00020. Epub 2019 Mar 7.

8.

Structural and dynamical rationale for fatty acid unsaturation in Escherichia coli.

Dodge GJ, Patel A, Jaremko KL, McCammon JA, Smith JL, Burkart MD.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6775-6783. doi: 10.1073/pnas.1818686116. Epub 2019 Mar 14.

9.

Allostery in Its Many Disguises: From Theory to Applications.

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.

10.

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.

Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE.

Biophys J. 2019 Jan 22;116(2):205-214. doi: 10.1016/j.bpj.2018.09.035. Epub 2018 Dec 8.

PMID:
30606449
11.

Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria.

Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA.

Chem Biol Drug Des. 2019 Apr;93(4):647-652. doi: 10.1111/cbdd.13462. Epub 2019 Feb 19.

PMID:
30570806
12.

Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.

Q Rev Biophys. 2018;51. pii: e91. doi: 10.1017/S0033583518000070. Epub 2018 Aug 3.

13.

Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements.

Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11129-11137. doi: 10.1073/pnas.1807624115. Epub 2018 Oct 9.

14.

A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif.

Utesch T, de Miguel Catalina A, Schattenberg C, Paege N, Schmieder P, Krause E, Miao Y, McCammon JA, Meyer V, Jung S, Mroginski MA.

mSphere. 2018 Oct 3;3(5). pii: e00377-18. doi: 10.1128/mSphere.00377-18.

15.

pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study.

Mermelstein DJ, McCammon JA, Walker RC.

J Mol Recognit. 2019 Mar;32(3):e2765. doi: 10.1002/jmr.2765. Epub 2018 Sep 27.

PMID:
30264484
16.

Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations.

Ricci CG, McCammon JA.

J Phys Chem B. 2018 Dec 13;122(49):11695-11701. doi: 10.1021/acs.jpcb.8b07773. Epub 2018 Oct 9.

PMID:
30252476
17.

Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases.

Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD.

Chembiochem. 2019 Jan 18;20(2):147-152. doi: 10.1002/cbic.201800439. Epub 2018 Nov 9.

PMID:
30194895
18.

RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations.

Guan W, Cheng X, Huang J, Huber G, Li W, McCammon JA, Zhang B.

Comput Phys Commun. 2018 Jun;227:99-108. doi: 10.1016/j.cpc.2018.02.005. Epub 2018 Feb 16.

19.

Ensemble Docking in Drug Discovery.

Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC.

Biophys J. 2018 May 22;114(10):2271-2278. doi: 10.1016/j.bpj.2018.02.038. Epub 2018 Mar 30. Review.

20.

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC.

J Comput Chem. 2018 Jul 15;39(19):1354-1358. doi: 10.1002/jcc.25187. Epub 2018 Mar 12.

PMID:
29532496
21.

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor.

Miao Y, McCammon JA.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3036-3041. doi: 10.1073/pnas.1800756115. Epub 2018 Mar 5.

22.

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

Huang YM, McCammon JA, Miao Y.

J Chem Theory Comput. 2018 Apr 10;14(4):1853-1864. doi: 10.1021/acs.jctc.7b01226. Epub 2018 Mar 12.

23.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.

Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA.

Front Mol Biosci. 2018 Feb 12;5:13. doi: 10.3389/fmolb.2018.00013. eCollection 2018. Review.

24.

Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA.

Biochemistry. 2018 Mar 6;57(9):1533-1541. doi: 10.1021/acs.biochem.7b01248. Epub 2018 Feb 15.

25.

Remarkable similarity in Plasmodium falciparum and Plasmodium vivax geranylgeranyl diphosphate synthase dynamics and its implication for antimalarial drug design.

Venkatramani A, Gravina Ricci C, Oldfield E, McCammon JA.

Chem Biol Drug Des. 2018 Jun;91(6):1068-1077. doi: 10.1111/cbdd.13170. Epub 2018 Feb 4.

26.

Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity.

Mouchlis VD, Chen Y, McCammon JA, Dennis EA.

J Am Chem Soc. 2018 Mar 7;140(9):3285-3291. doi: 10.1021/jacs.7b12045. Epub 2018 Feb 26.

27.

HIERARCHICAL ORTHOGONAL MATRIX GENERATION AND MATRIX-VECTOR MULTIPLICATIONS IN RIGID BODY SIMULATIONS.

Fang F, Huang J, Huber G, McCammon JA, Zhang BO.

SIAM J Sci Comput. 2018;40(3):A1345-A1361. doi: 10.1137/17M1117744. Epub 2018 May 10.

28.

Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

Huang YM, Huber GA, Wang N, Minteer SD, McCammon JA.

Protein Sci. 2018 Feb;27(2):463-471. doi: 10.1002/pro.3338. Epub 2017 Nov 21.

29.

Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins.

Jaremko MJ, Lee DJ, Patel A, Winslow V, Opella SJ, McCammon JA, Burkart MD.

Biochemistry. 2017 Oct 10;56(40):5269-5273. doi: 10.1021/acs.biochem.7b00884. Epub 2017 Oct 2.

30.

Improvements to the APBS biomolecular solvation software suite.

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA.

Protein Sci. 2018 Jan;27(1):112-128. doi: 10.1002/pro.3280. Epub 2017 Oct 24.

31.

Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9.

Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA.

J Am Chem Soc. 2017 Nov 15;139(45):16028-16031. doi: 10.1021/jacs.7b05313. Epub 2017 Aug 7.

32.

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations.

Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7260-7265. doi: 10.1073/pnas.1707645114. Epub 2017 Jun 26. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8944.

33.

Mapping the allosteric sites of the A2A adenosine receptor.

Caliman AD, Miao Y, McCammon JA.

Chem Biol Drug Des. 2018 Jan;91(1):5-16. doi: 10.1111/cbdd.13053. Epub 2017 Jul 19.

34.

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA.

J Phys Chem B. 2017 Jul 13;121(27):6538-6548. doi: 10.1021/acs.jpcb.7b04113. Epub 2017 Jun 27.

35.

Effect of donor atom identity on metal-binding pharmacophore coordination.

Dick BL, Patel A, McCammon JA, Cohen SM.

J Biol Inorg Chem. 2017 Jun;22(4):605-613. doi: 10.1007/s00775-017-1454-3. Epub 2017 Apr 7.

36.

Activation mechanisms of the first sphingosine-1-phosphate receptor.

Caliman AD, Miao Y, McCammon JA.

Protein Sci. 2017 Jun;26(6):1150-1160. doi: 10.1002/pro.3165. Epub 2017 Apr 12.

37.

Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors.

O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E.

Chembiochem. 2017 May 18;18(10):914-920. doi: 10.1002/cbic.201700052. Epub 2017 Apr 7.

38.

NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors.

Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT.

Chem Biol Drug Des. 2017 Sep;90(3):327-344. doi: 10.1111/cbdd.12962. Epub 2017 Mar 6.

39.

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.

Miao Y, McCammon JA.

Annu Rep Comput Chem. 2017;13:231-278. doi: 10.1016/bs.arcc.2017.06.005. Epub 2017 Aug 10.

40.

Gaussian Accelerated Molecular Dynamics in NAMD.

Pang YT, Miao Y, Wang Y, McCammon JA.

J Chem Theory Comput. 2017 Jan 10;13(1):9-19. doi: 10.1021/acs.jctc.6b00931. Epub 2016 Dec 30.

41.

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.

Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA.

ACS Cent Sci. 2016 Oct 26;2(10):756-763. Epub 2016 Sep 9.

42.

Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor.

Miao Y, McCammon JA.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12162-12167. Epub 2016 Oct 10.

43.

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor.

Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C.

Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):E5675-84. doi: 10.1073/pnas.1612353113. Epub 2016 Sep 6.

44.

Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase.

G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA.

Biochemistry. 2016 Sep 13;55(36):5180-90. doi: 10.1021/acs.biochem.6b00398. Epub 2016 Sep 1.

45.

Autobiography of J. Andrew McCammon.

McCammon JA.

J Phys Chem B. 2016 Aug 25;120(33):8057-60. doi: 10.1021/acs.jpcb.6b00834. No abstract available.

46.

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.

Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA.

J Chem Phys. 2016 Aug 7;145(5):054114. doi: 10.1063/1.4959971.

47.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

Miao Y, McCammon JA.

Mol Simul. 2016;42(13):1046-1055. Epub 2016 Jul 5.

48.

G-protein coupled receptors: advances in simulation and drug discovery.

Miao Y, McCammon JA.

Curr Opin Struct Biol. 2016 Dec;41:83-89. doi: 10.1016/j.sbi.2016.06.008. Epub 2016 Jun 22. Review.

49.

Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A2.

Mouchlis VD, Morisseau C, Hammock BD, Li S, McCammon JA, Dennis EA.

Bioorg Med Chem. 2016 Oct 15;24(20):4801-4811. doi: 10.1016/j.bmc.2016.05.009. Epub 2016 May 10.

50.

Hybrid finite element and Brownian dynamics method for charged particles.

Huber GA, Miao Y, Zhou S, Li B, McCammon JA.

J Chem Phys. 2016 Apr 28;144(16):164107. doi: 10.1063/1.4947086.

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