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Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.
Sultan MM, Wayment-Steele HK, Pande VS. Sultan MM, et al. J Chem Theory Comput. 2018 Apr 10;14(4):1887-1894. doi: 10.1021/acs.jctc.8b00025. Epub 2018 Mar 19. J Chem Theory Comput. 2018. PMID: 29529369
A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.
Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS. Husic BE, et al. Among authors: sultan mm. J Chem Theory Comput. 2018 Feb 13;14(2):1071-1082. doi: 10.1021/acs.jctc.7b01004. Epub 2018 Jan 24. J Chem Theory Comput. 2018. PMID: 29253336
Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.
Sultan MM, Kiss G, Shukla D, Pande VS. Sultan MM, et al. J Chem Theory Comput. 2014 Dec 9;10(12):5217-5223. doi: 10.1021/ct500353m. Epub 2014 Oct 22. J Chem Theory Comput. 2014. PMID: 25516725 Free PMC article.
Optimized parameter selection reveals trends in Markov state models for protein folding.
Husic BE, McGibbon RT, Sultan MM, Pande VS. Husic BE, et al. Among authors: sultan mm. J Chem Phys. 2016 Nov 21;145(19):194103. doi: 10.1063/1.4967809. J Chem Phys. 2016. PMID: 27875868 Free PMC article.
MSMBuilder: Statistical Models for Biomolecular Dynamics.
Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS. Harrigan MP, et al. Among authors: sultan mm. Biophys J. 2017 Jan 10;112(1):10-15. doi: 10.1016/j.bpj.2016.10.042. Biophys J. 2017. PMID: 28076801 Free PMC article.
Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.
Sultan MM, Pande VS. Sultan MM, et al. J Phys Chem B. 2018 May 31;122(21):5291-5299. doi: 10.1021/acs.jpcb.7b06896. Epub 2017 Oct 3. J Phys Chem B. 2018. PMID: 28938073
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain.
Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS. Sultan MM, et al. Sci Rep. 2017 Nov 15;7(1):15604. doi: 10.1038/s41598-017-10697-0. Sci Rep. 2017. PMID: 29142210 Free PMC article.
Automated design of collective variables using supervised machine learning.
Sultan MM, Pande VS. Sultan MM, et al. J Chem Phys. 2018 Sep 7;149(9):094106. doi: 10.1063/1.5029972. J Chem Phys. 2018. PMID: 30195289
Variational encoding of complex dynamics.
Hernández CX, Wayment-Steele HK, Sultan MM, Husic BE, Pande VS. Hernández CX, et al. Among authors: sultan mm. Phys Rev E. 2018 Jun;97(6-1):062412. doi: 10.1103/PhysRevE.97.062412. Phys Rev E. 2018. PMID: 30011547 Free PMC article.
Towards simple kinetic models of functional dynamics for a kinase subfamily.
Sultan MM, Kiss G, Pande VS. Sultan MM, et al. Nat Chem. 2018 Sep;10(9):903-909. doi: 10.1038/s41557-018-0077-9. Epub 2018 Jul 9. Nat Chem. 2018. PMID: 29988151
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