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Items: 1 to 20 of 272

1.

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.

2.

Automated design of collective variables using supervised machine learning.

Sultan MM, Pande VS.

J Chem Phys. 2018 Sep 7;149(9):094106. doi: 10.1063/1.5029972.

PMID:
30195289
3.

Engineering a Single-Agent Cytokine/Antibody Fusion That Selectively Expands Regulatory T Cells for Autoimmune Disease Therapy.

Spangler JB, Trotta E, Tomala J, Peck A, Young TA, Savvides CS, Silveria S, Votavova P, Salafsky J, Pande VS, Kovar M, Bluestone JA, Garcia KC.

J Immunol. 2018 Oct 1;201(7):2094-2106. doi: 10.4049/jimmunol.1800578. Epub 2018 Aug 13.

PMID:
30104245
4.

Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors.

Sinitskiy AV, Pande VS.

Biophys J. 2018 Sep 4;115(5):841-852. doi: 10.1016/j.bpj.2018.06.023. Epub 2018 Jun 28.

PMID:
30029773
5.

Variational encoding of complex dynamics.

Hernández CX, Wayment-Steele HK, Sultan MM, Husic BE, Pande VS.

Phys Rev E. 2018 Jun;97(6-1):062412. doi: 10.1103/PhysRevE.97.062412.

PMID:
30011547
6.

Towards simple kinetic models of functional dynamics for a kinase subfamily.

Sultan MM, Kiss G, Pande VS.

Nat Chem. 2018 Sep;10(9):903-909. doi: 10.1038/s41557-018-0077-9. Epub 2018 Jul 9.

PMID:
29988151
7.

Solving the RNA design problem with reinforcement learning.

Eastman P, Shi J, Ramsundar B, Pande VS.

PLoS Comput Biol. 2018 Jun 21;14(6):e1006176. doi: 10.1371/journal.pcbi.1006176. eCollection 2018 Jun.

8.

Communication: Adaptive boundaries in multiscale simulations.

Wagoner JA, Pande VS.

J Chem Phys. 2018 Apr 14;148(14):141104. doi: 10.1063/1.5025826.

9.

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.

Sultan MM, Wayment-Steele HK, Pande VS.

J Chem Theory Comput. 2018 Apr 10;14(4):1887-1894. doi: 10.1021/acs.jctc.8b00025. Epub 2018 Mar 19.

PMID:
29529369
10.

REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment.

Yang H, Staveness D, Ryckbosch SM, Axtman AD, Loy BA, Barnes AB, Pande VS, Schaefer J, Wender PA, Cegelski L.

ACS Cent Sci. 2018 Jan 24;4(1):89-96. doi: 10.1021/acscentsci.7b00475. Epub 2018 Jan 2.

11.

Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.

Sinitskiy AV, Pande VS.

J Chem Phys. 2018 Jan 28;148(4):044111. doi: 10.1063/1.5005058.

PMID:
29390806
12.

Markov State Models: From an Art to a Science.

Husic BE, Pande VS.

J Am Chem Soc. 2018 Feb 21;140(7):2386-2396. doi: 10.1021/jacs.7b12191. Epub 2018 Feb 2. Review.

PMID:
29323881
13.

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.

Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS.

J Chem Theory Comput. 2018 Feb 13;14(2):1071-1082. doi: 10.1021/acs.jctc.7b01004. Epub 2018 Jan 24.

PMID:
29253336
14.

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain.

Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS.

Sci Rep. 2017 Nov 15;7(1):15604. doi: 10.1038/s41598-017-10697-0.

15.

Note: MSM lag time cannot be used for variational model selection.

Husic BE, Pande VS.

J Chem Phys. 2017 Nov 7;147(17):176101. doi: 10.1063/1.5002086.

16.

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains.

Lee FL, Barati Farimani A, Gu KL, Yan H, Toney MF, Bao Z, Pande VS.

J Phys Chem Lett. 2017 Nov 16;8(22):5479-5486. doi: 10.1021/acs.jpclett.7b02360. Epub 2017 Oct 30.

PMID:
29065685
17.

Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core.

Sinitskiy AV, Pande VS.

J Chem Theory Comput. 2017 Nov 14;13(11):5496-5505. doi: 10.1021/acs.jctc.7b00817. Epub 2017 Oct 31.

PMID:
29019687
18.

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.

Sultan MM, Pande VS.

J Phys Chem B. 2018 May 31;122(21):5291-5299. doi: 10.1021/acs.jpcb.7b06896. Epub 2017 Oct 3.

PMID:
28938073
19.

Modeling the mechanism of CLN025 beta-hairpin formation.

McKiernan KA, Husic BE, Pande VS.

J Chem Phys. 2017 Sep 14;147(10):104107. doi: 10.1063/1.4993207.

20.

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.

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