Alan Grossfield

发表

Validating and improving elastic network models with molecular dynamics simulations

Tod D Romo, Alan Grossfield, A. Grossfield, 2011, Proteins.

Loos: A Toolkit for Analyzing Molecular Simulations and Making New Tools

Alan Grossfield, Tod D. Romo, 2016 .

Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation.

Tod D Romo, Alan Grossfield, A. Grossfield, 2011, Journal of chemical theory and computation.

Quantifying uncertainty and sampling quality in biomolecular simulations.

Alan Grossfield, Daniel M Zuckerman, D. Zuckerman, 2009, Annual reports in computational chemistry.

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations

Daniel M. Zuckerman, Andrew J. Schultz, Alan Grossfield, 2018 .

Elastic Network Models are Robust to Variations in Formalism.

Tod D Romo, Alan Grossfield, Nicholas Leioatts, 2012, Journal of chemical theory and computation.

Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

Alan Grossfield, Tod D. Romo, Nicholas Leioatts, 2014, J. Comput. Chem..

New and Notable

Alan Grossfield, Tod D. Romo, J. Scheuer, 2000 .

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].

Alan Grossfield, Daniel M Zuckerman, Paul N Patrone, 2018, Living journal of computational molecular science.

LOOS: An extensible platform for the structural analysis of simulations

Alan Grossfield, Tod D. Romo, A. Grossfield, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

LOOS: A Suite of Tools to Analyze Molecular Dynamics Simulations

Alan Grossfield, Tod D. Romo, 2020 .

Loos: A Tool for Making New Tools for Analyzing Molecular Simulations

Alan Grossfield, Tod D. Romo, 2013 .

Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

Robert S. Germain, Mark Giampapa, Ruhong Zhou, 2006, International Conference on Computational Science.

Loos, a Better Tool to Analyze Molecular Dynamics Simulations

Alan Grossfield, Tod D. Romo, 2021 .

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

David H. Mathews, Alan Grossfield, Asaminew H. Aytenfisu, 2017, Journal of chemical theory and computation.

Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin.

Alan Grossfield, A. Grossfield, Joshua N. Horn, 2014, Advances in experimental medicine and biology.

Retinal counterion switch mechanism in vision evaluated by molecular simulations.

Alan Grossfield, Karina Martínez-Mayorga, M. Pitman, 2006, Journal of the American Chemical Society.

Convergence of molecular dynamics simulations of membrane proteins

Alan Grossfield, M. Pitman, S. Feller, 2007, Proteins.

Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics.

Tod D Romo, Alan Grossfield, M. Pitman, 2010, Biophysical journal.

Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations.

Alan Grossfield, A. Grossfield, 2011, Biochimica et biophysica acta.

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

Alan Grossfield, Dian Jiao, Pengyu Ren, 2006, The journal of physical chemistry. B.

Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.

Tod D Romo, Alan Grossfield, A. Grossfield, 2014, Biophysical journal.

Implicit Modeling of Membranes

Alan Grossfield, A. Grossfield, 2008 .

Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment.

Frank Suits, Alan Grossfield, F. Suits, 2005, Journal of the American Chemical Society.

Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.

Alan Grossfield, M. Pitman, S. Feller, 2008, Journal of molecular biology.

A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

Alan Grossfield, M. Pitman, S. Feller, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations

George Khelashvili, Harel Weinstein, Alan Grossfield, 2009, Proteins.

Base flipping of the thymine dimer in duplex DNA.

Alan Grossfield, Olaf Wiest, Lauren L O'Neil, 2007, The journal of physical chemistry. B.

Role of solvent in determining conformational preferences of alanine dipeptide in water.

Alan Grossfield, Rohit V Pappu, Alexander N Drozdov, 2004, Journal of the American Chemical Society.

A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids

Alan Grossfield, Michael C. Pitman, M. Pitman, 2006 .

Structural Basis of G Protein-coupled Receptor-Gi Protein Interaction

Alan Grossfield, Nicholas Leioatts, Dow P Hurst, 2014, The Journal of Biological Chemistry.

Chapter 5 Implicit Modeling of Membranes

Alan Grossfield, A. Grossfield, 2008 .

A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor*

Tod D Romo, Alan Grossfield, Dow P Hurst, 2010, The Journal of Biological Chemistry.