J
Josh V. Vermaas
Researcher at National Renewable Energy Laboratory
Publications - 64
Citations - 1576
Josh V. Vermaas is an academic researcher from National Renewable Energy Laboratory. The author has contributed to research in topics: Chemistry & Biology. The author has an hindex of 18, co-authored 44 publications receiving 1046 citations. Previous affiliations of Josh V. Vermaas include Michigan State University & University of Illinois at Urbana–Champaign.
Papers
More filters
Journal ArticleDOI
Mechanism of lignin inhibition of enzymatic biomass deconstruction
Josh V. Vermaas,Loukas Petridis,Xianghong Qi,Roland Schulz,Roland Schulz,Benjamin Lindner,Jeremy C. Smith +6 more
TL;DR: Lignin binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.
Journal ArticleDOI
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
Atanu Acharya,Rupesh Agarwal,Rupesh Agarwal,Matthew B. Baker,Jerome Baudry,Debsindhu Bhowmik,Swen Boehm,Kendall G. Byler,Samuel Yen-Chi Chen,Leighton Coates,Connor J. Cooper,Connor J. Cooper,Omar Demerdash,Isabella Daidone,John D. Eblen,John D. Eblen,Sally R. Ellingson,Stefano Forli,Jens Glaser,James C. Gumbart,John A. Gunnels,Oscar Hernandez,Stephan Irle,Stephan Irle,Daniel W. Kneller,Andrey Kovalevsky,Jeffrey M. Larkin,Travis J Lawrence,Scott LeGrand,Shih-Hsien Liu,Shih-Hsien Liu,Julie C. Mitchell,Gilchan Park,Jerry M. Parks,Jerry M. Parks,Anna Pavlova,Loukas Petridis,Loukas Petridis,Duncan Poole,Line Pouchard,Arvind Ramanathan,David M. Rogers,Diogo Santos-Martins,Aaron Scheinberg,Ada Sedova,Y. Shen,Y. Shen,Jeremy C. Smith,Jeremy C. Smith,Micholas Dean Smith,Micholas Dean Smith,Carlos Soto,A. Tsaris,Mathialakan Thavappiragasam,Andreas F. Tillack,Josh V. Vermaas,V. Q. Vuong,V. Q. Vuong,Junqi Yin,Shinjae Yoo,Mai Zahran,Laura Zanetti-Polzi +61 more
TL;DR: A supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking is presented, including the use of quantum mechanical, machine learning, and artificial intelligence methods to cluster MD trajectories and rescore docking poses.
Journal ArticleDOI
Passive membrane transport of lignin-related compounds.
Josh V. Vermaas,Richard A. Dixon,Fang Chen,Shawn D. Mansfield,Wout Boerjan,John Ralph,Michael F. Crowley,Gregg T. Beckham +7 more
TL;DR: It is predicted that passive transport processes in plants and bacteria for uncharged aromatic compounds are likely sufficient for lignin biosynthesis and catabolism, thus implying that membrane translocation rates are controlled by compound delivery and utilization rates and membrane concentration gradients.
Journal ArticleDOI
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
Yifei Qi,Xi Cheng,Jumin Lee,Josh V. Vermaas,Taras V. Pogorelov,Emad Tajkhorshid,Soohyung Park,Jeffery B. Klauda,Wonpil Im +8 more
TL;DR: CHARMM-GUI HMMM Builder is developed to provide users with ready-to-go input files for simulating HMMm membrane systems with/without proteins and is expected to be a useful tool in studying membranes systems with enhanced lipid diffusion.
Journal Article
Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases B
TL;DR: In this paper, the effect of oxidation on the structure of crystalline cellulose was examined using molecular simulation, and the results indicated that the equilibrium between the two reducing end oxidized products, favoring the linear aldonic acid, may increase product inhibition, which would in turn reduce processive substrate turnover.