Finding Our Way in the Dark Proteome.
J Am Chem Soc. 2016 Aug 10;138(31):9730-42. doi: 10.1021/jacs.6b06543. Epub 2016 Jul 19. Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande…
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Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
PLoS Comput Biol. 2016 Jun 23;12(6):e1004728. doi: 10.1371/journal.pcbi.1004728. eCollection 2016. Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD. The rapidly expanding body of available genomic and protein…
Read moreEnsembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept …
Read moreMarkov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.
Biophys J. 2016 Apr 26;110(8):1716-9. doi: 10.1016/j.bpj.2016.03.026. Schwantes CR, Shukla D, Pande VS After reanalyzing simulations of NuG2-a designed mutant of protein G-generated by Lindorff-Larsen et al. with time structure-based independent…
Read moreConformational heterogeneity of the calmodulin binding interface.
Nat Commun. 2016 Apr 4;7:10910. doi: 10.1038/ncomms10910. Shukla D ,Peck A , Pande VS Finally, our model predicts a novel binding interface that is well-populated in the Ca(2+)-bound regime and, thus, a…
Read moreUsing Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.
J Phys Chem B. 2016 Feb 11;120(5):926-35. doi: 10.1021/acs.jpcb.5b11767. Epub 2016 Feb 1. Zhou G, Voelz VA. Salt-bridge interactions play an important role in stabilizing many protein structures, and have…
Read moreInsights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.
Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consi…
Read moreFAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.
Molecular dynamics simulations are a powerful means of understanding conformational changes. However, it is still difficult to simulate biologically relevant time scales without the use of specialized supercomputers. Here, we introduce a goal-oriented sampling method, called fluctuation amplification of specific traits (FAST), for extending the capabilities of commodity hardware. This algorithm rapidly searches conformational space for structures with desired properties by balancing trade-offs…
Read moreMDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.
Biophys J. 2015 Oct 20;109(8):1528-32. doi: 10.1016/j.bpj.2015.08.015. McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS As molecular dynamics…
Read moreHeat dissipation guides activation in signaling proteins.
Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10377-82. doi: 10.1073/pnas.1501804112. Epub 2015 Aug 3. Weber JK, Shukla D, Pande VS Life is fundamentally a nonequilibrium phenomenon. At the…
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