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Items: 1 to 50 of 277

1.

Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ1) receptor selective ligands.

Uprety R, Váradi A, Allaoa A, Redel-Traub GN, Palmer TC, Feinberg EN, Ferris AC, Pande VS, Pasternak GW, Majumdar S.

Eur J Med Chem. 2019 Feb 15;164:241-251. doi: 10.1016/j.ejmech.2018.12.048. Epub 2018 Dec 22.

PMID:
30597325
2.

PotentialNet for Molecular Property Prediction.

Feinberg EN, Sur D, Wu Z, Husic BE, Mai H, Li Y, Sun S, Yang J, Ramsundar B, Pande VS.

ACS Cent Sci. 2018 Nov 28;4(11):1520-1530. doi: 10.1021/acscentsci.8b00507. Epub 2018 Nov 2.

3.

Note: Variational encoding of protein dynamics benefits from maximizing latent autocorrelation.

Wayment-Steele HK, Pande VS.

J Chem Phys. 2018 Dec 7;149(21):216101. doi: 10.1063/1.5043303.

PMID:
30525733
4.

Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling.

Subedi GP, Sinitskiy AV, Roberts JT, Patel KR, Pande VS, Barb AW.

Structure. 2019 Jan 2;27(1):55-65.e3. doi: 10.1016/j.str.2018.09.010. Epub 2018 Oct 25.

PMID:
30482728
5.

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T.

J Chem Phys. 2018 Nov 14;149(18):180901. doi: 10.1063/1.5052551.

PMID:
30441927
6.

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.

7.

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
8.

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
9.

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.

10.

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
11.

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
12.

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.

13.

Communication: Adaptive boundaries in multiscale simulations.

Wagoner JA, Pande VS.

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

14.

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
15.

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.

16.

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.

17.

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
18.

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
19.

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.

20.

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.

21.

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
22.

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
23.

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
24.

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.

25.

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.

26.

Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders.

Yi B, Jahangir A, Evans AK, Briggs D, Ravina K, Ernest J, Farimani AB, Sun W, Rajadas J, Green M, Feinberg EN, Pande VS, Shamloo M.

PLoS One. 2017 Jul 26;12(7):e0180319. doi: 10.1371/journal.pone.0180319. eCollection 2017.

27.

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.

M Sultan M, Pande VS.

J Chem Theory Comput. 2017 Jun 13;13(6):2440-2447. doi: 10.1021/acs.jctc.7b00182. Epub 2017 May 9.

PMID:
28383914
28.

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors.

Sinitskiy AV, Stanley NH, Hackos DH, Hanson JE, Sellers BD, Pande VS.

Sci Rep. 2017 Apr 5;7:44578. doi: 10.1038/srep44578.

29.

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.

Harrigan MP, McKiernan KA, Shanmugasundaram V, Denny RA, Pande VS.

Sci Rep. 2017 Apr 4;7(1):632. doi: 10.1038/s41598-017-00256-y.

30.

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS.

J Phys Chem B. 2017 Apr 27;121(16):4023-4039. doi: 10.1021/acs.jpcb.7b02320. Epub 2017 Apr 6.

PMID:
28306259
31.

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.

Shi J, Nobrega RP, Schwantes C, Kathuria SV, Bilsel O, Matthews CR, Lane TJ, Pande VS.

Sci Rep. 2017 Mar 8;7:44116. doi: 10.1038/srep44116.

32.

Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes.

Ryckbosch SM, Wender PA, Pande VS.

Nat Commun. 2017 Feb 23;8(1):6. doi: 10.1038/s41467-016-0015-8.

33.

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding.

Husic BE, Pande VS.

J Chem Theory Comput. 2017 Mar 14;13(3):963-967. doi: 10.1021/acs.jctc.6b01238. Epub 2017 Feb 17.

PMID:
28195713
34.

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

Zhang B, Kilburg D, Eastman P, Pande VS, Gallicchio E.

J Comput Chem. 2017 Apr 15;38(10):740-752. doi: 10.1002/jcc.24745. Epub 2017 Feb 4.

PMID:
28160511
35.

Identification of simple reaction coordinates from complex dynamics.

McGibbon RT, Husic BE, Pande VS.

J Chem Phys. 2017 Jan 28;146(4):044109. doi: 10.1063/1.4974306.

36.

MSMBuilder: Statistical Models for Biomolecular Dynamics.

Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS.

Biophys J. 2017 Jan 10;112(1):10-15. doi: 10.1016/j.bpj.2016.10.042.

37.

Optimized parameter selection reveals trends in Markov state models for protein folding.

Husic BE, McGibbon RT, Sultan MM, Pande VS.

J Chem Phys. 2016 Nov 21;145(19):194103.

38.

Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.

McKiernan KA, Wang LP, Pande VS.

J Chem Theory Comput. 2016 Dec 13;12(12):5960-5967. Epub 2016 Nov 21.

PMID:
27786477
39.

Advanced Potential Energy Surfaces for Molecular Simulation.

Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T.

J Phys Chem B. 2016 Sep 22;120(37):9811-32. doi: 10.1021/acs.jpcb.6b06414. Review.

PMID:
27513316
40.

Corrigendum: Conformational heterogeneity of the calmodulin binding interface.

Shukla D, Peck A, Pande VS.

Nat Commun. 2016 Aug 10;7:12318. doi: 10.1038/ncomms12318. No abstract available.

41.

Transition path theory analysis of c-Src kinase activation.

Meng Y, Shukla D, Pande VS, Roux B.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8. doi: 10.1073/pnas.1602790113. Epub 2016 Aug 1.

42.

Finding Our Way in the Dark Proteome.

Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T.

J Am Chem Soc. 2016 Aug 10;138(31):9730-42. doi: 10.1021/jacs.6b06543. Epub 2016 Jul 19.

43.

Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase.

Peck A, Sunden F, Andrews LD, Pande VS, Herschlag D.

J Mol Biol. 2016 Jul 3;428(13):2758-68. doi: 10.1016/j.jmb.2016.05.007. Epub 2016 May 14.

44.

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.

Schwantes CR, Shukla D, Pande VS.

Biophys J. 2016 Apr 26;110(8):1716-1719. doi: 10.1016/j.bpj.2016.03.026.

45.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models.

Dodani SC, Kiss G, Cahn JK, Su Y, Pande VS, Arnold FH.

Nat Chem. 2016 May;8(5):419-25. doi: 10.1038/nchem.2474. Epub 2016 Mar 21.

46.

Conformational heterogeneity of the calmodulin binding interface.

Shukla D, Peck A, Pande VS.

Nat Commun. 2016 Apr 4;7:10910. doi: 10.1038/ncomms10910. Erratum in: Nat Commun. 2016 Aug 10;7:12318.

47.

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.

Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ.

Nat Genet. 2016 Feb;48(2):117-25. doi: 10.1038/ng.3471. Epub 2015 Dec 21.

48.

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.

Wang LP, McGibbon RT, Pande VS, Martinez TJ.

J Chem Theory Comput. 2016 Feb 9;12(2):638-49. doi: 10.1021/acs.jctc.5b00830. Epub 2016 Jan 19.

PMID:
26683346
49.

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL 3rd, MacKerell AD Jr, Klauda JB, Im W.

J Chem Theory Comput. 2016 Jan 12;12(1):405-13. doi: 10.1021/acs.jctc.5b00935. Epub 2015 Dec 3.

50.

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.

Harrigan MP, Shukla D, Pande VS.

J Chem Theory Comput. 2015 Mar 10;11(3):1094-101. doi: 10.1021/ct5010017.

PMID:
26579759

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