Author

J. V. Vermaas

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 5 Bioengineering· 1

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 4 Assay:cryo-EM· 2 Approach:deep learning· 2 Approach:experimental assay· 2 Approach:mechanistic / dynamical model· 2 Approach:statistical model· 2 Assay:structural biology· 2 Organism:bacteria (other)· 1

Frequent Co-Authors

D. Sarkar· 4 shared A. Singharoy· 2 shared J. W. Vant· 2 shared A. A. Golosov· 1 shared A. Acharya· 1 shared A. Kovalevsky· 1 shared A. Pavlova· 1 shared B. Yao· 1 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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4 shared papersBiophysics

D. Sarkar

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

S. Raza, D. Sarkar, L. J. G. Chan, J. Mae, M. Sutter, C. J. Petzold, C. A. Kerfeld, C. Y. Ralston, S. Gupta, J. V. Vermaas

The paper compares pore structure and dynamics in bacterial microcompartment shell proteins under different geometries using molecular modeling and simulations.

bioRxiv · Mar 12, 2024Biophysics

Structural Remodeling of Fungal Cell Wall Promotes Resistance to Echinocandins

M. C. Dickwella Widanage, I. Gautam, D. Sarkar, F. Mentink-Vigier, J. V. Vermaas, T. Fontaine, J.-P. Latge, P. Wang, T. Wang

The paper investigates how fungal cell wall remodeling in response to echinocandins leads to drug resistance by altering carbohydrate polymer assembly and physical properties.

bioRxiv · Aug 9, 2023Biophysics

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

D. Sarkar, H. Lee, J. W. Vant, M. Turilli, J. V. Vermaas, S. Jha, A. Singharoy

This paper introduces an adaptive ensemble refinement method for protein structures using MDFF and RADICAL-Cybertools, improving correlation with cryo-EM density maps by 40%.

bioRxiv · Dec 7, 2021 · PreprintBiophysics

Data-guided Multi-Map variables for ensemble refinement of molecular movies

J. W. Vant, D. Sarkar, E. Streitwieser, G. Fiorin, R. D. Skeel, J. V. Vermaas, A. Singharoy

This paper introduces a method to refine molecular simulations using data-guided collective variables, showing improved free-energy estimates and structural accuracy compared to existing models.

The Journal of Chemical Physics · Dec 7, 2020Peer-reviewedBiophysics

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

A. Pavlova, D. L. Lynch, I. Daidone, L. Zanetti-Polzi, M. D. Smith, C. Chipot, D. W. Kneller, A. Kovalevsky, L. Coates, A. A. Golosov, C. J. Dickson, C. Velez-Vega, J. S. Duca, J. V. Vermaas, Y. T. Pang, , J. C. Gumbart

This study uses molecular dynamics simulations to investigate how inhibitor binding affects the protonation states of histidines in SARS-CoV-2 main protease, showing their impact on structural stability and inhibitor binding.

bioRxiv · Sep 7, 2020Biophysics

Characterizing Activity and Thermostability of GH5 Cellulase Chimeras from Mesophilic and Thermophilic Parents

F. Zheng, J. V. Vermaas, J. Zheng, Y. Wang, T. Tu, X. Wang, X. Xie, B. Yao, G. T. Beckham, H. Luo

This study creates GH5 cellulase hybrids from mesophilic and thermophilic parents to identify elements enhancing thermostability, finding improved thermal properties in some hybrids.

bioRxiv · Aug 1, 2018Bioengineering