J
James C. Gumbart
Researcher at Georgia Institute of Technology
Publications - 172
Citations - 21460
James C. Gumbart is an academic researcher from Georgia Institute of Technology. The author has contributed to research in topics: Chemistry & Biology. The author has an hindex of 38, co-authored 130 publications receiving 18761 citations. Previous affiliations of James C. Gumbart include University of Illinois at Urbana–Champaign & Argonne National Laboratory.
Papers
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Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
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Rapid parameterization of small molecules using the Force Field Toolkit.
TL;DR: The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design.
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Structural insight into the biogenesis of β-barrel membrane proteins
Nicholas Noinaj,Adam J. Kuszak,James C. Gumbart,Petra Lukacik,Hoshing Chang,Nicole C. Easley,Trevor Lithgow,Susan K. Buchanan +7 more
TL;DR: The structure of BamA is described, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi, which consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain.
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The adaptive biasing force method: everything you always wanted to know but were afraid to ask.
Jeffrey Comer,James C. Gumbart,Jérôme Hénin,Tony Lelièvre,Andrew Pohorille,Andrew Pohorille,Christophe Chipot +6 more
TL;DR: In this contribution, the adaptive biasing force algorithm is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability, and inherent limitations, as well as introducing novel extensions.
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Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome
Thomas Becker,Shashi Bhushan,Alexander Jarasch,Jean Paul Armache,Soledad Funes,Soledad Funes,Fabrice Jossinet,James C. Gumbart,Thorsten Mielke,Thorsten Mielke,Otto Berninghausen,Klaus Schulten,Eric Westhof,Reid Gilmore,Elisabet C. Mandon,Roland Beckmann +15 more
TL;DR: Subnanometer-resolution cryo–electron microscopy structures of eukaryotic ribosome-Sec61 complexes are determined and it is found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site.