Author details

Full Name

Michael E Wall

Affiliation

ORCID

Career Start Year

1995

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36601807	Molecular-dynamics simulation methods for macromolecular crystallography.	Acta Crystallogr D Struct Biol	2023
37748833	Molecular-dynamics simulations of macromolecular diffraction, part I: Preparation of protein crystal simulations.		2023
37748827	Interpreting macromolecular diffraction through simulation.		2023
37748824	Molecular-dynamics simulations of macromolecular diffraction, part II: Analysis of protein crystal simulations.		2023
37645800	Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.	bioRxiv	2023
36813723	Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics.		2023
37369071	Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.	J Am Chem Soc	2023
35148093	Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.	Journal of Chemical Theory and Computation	2022
34258328	Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.	Struct Dyn	2021
30834751	Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.	Journal of the American Chemical Society	2019
31801874	Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.	Proc Natl Acad Sci U S A	2019
31867408	Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.	Struct Dyn	2019
30994934	Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.	Journal of Computational Chemistry	2019
29455056	Bringing diffuse X-ray scattering into focus.	Curr Opin Struct Biol	2018
29765607	Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.	IUCrJ	2018
29765599	Interactions that know no boundaries.	IUCrJ	2018
27824914	Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions.	PLoS ONE	2016
27437111	Quantum crystallographic charge density of urea.	IUCrJ	2016
27334148	Graph-based linear scaling electronic structure theory.	Journal of Chemical Physics	2016
27267207	Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.	Journal of Chemical Theory and Computation	2016
27035972	Measuring and modeling diffuse scattering in protein X-ray crystallography.	Proc Natl Acad Sci U S A	2016
26574255	Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.	Journal of Chemical Theory and Computation	2015
26716953	The eighth q-bio conference: meeting report and special issue preface.	Physical Biology	2015
26249347	Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.	Acta Crystallogr D Biol Crystallogr	2015
24507780	Diffuse X-ray scattering to model protein motions.	Structure	2014
25453071	Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.	Proc Natl Acad Sci U S A	2014
25075709	The Seventh q-bio Conference: meeting report and preface.	Physical Biology	2014
23735417	Special section dedicated to The Sixth q-bio Conference: meeting report and preface.	Physical Biology	2013
23424147	Detection of protein catalytic sites in the biomedical literature.	Pac Symp Biocomput	2013
22052504	Predicting binding sites by analyzing allosteric effects.	Methods in Molecular Biology	2012
22393388	Text mining improves prediction of protein functional sites.	PLoS One	2012
23046792	Literature mining of protein-residue associations with graph rules learned through distant supervision.	J Biomed Semantics	2012
22131910	Genome majority vote improves gene predictions.	PLoS Computational Biology	2011
21342528	Consistency of gene starts among Burkholderia genomes.	BMC Genomics	2011
21329703	Structure-function relations are subtle in genetic regulatory networks.		2011
21832800	Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.	Physical Biology	2011
21073232	The Third q-bio Conference on Cellular Information Processing.	IET Systems Biology	2010
20019803	Model of transcriptional activation by MarA in Escherichia coli.	PLoS Computational Biology	2009
19488705	Methods and software for diffuse X-ray scattering from protein crystals.	Methods in Molecular Biology	2009
18234095	Fast dynamics perturbation analysis for prediction of protein functional sites.	BMC Structural Biology	2008
19045824	Determinants of bistability in induction of the Escherichia coli lac operon.	IET Syst Biol	2008
19045816	Selected papers from the First q-bio Conference on Cellular Information Processing.	IET Systems Biology	2008
18352046	Hidden structure in protein energy landscapes.		2008
18514222	Activation of the Escherichia coli marA/soxS/rob regulon in response to transcriptional activator concentration.	Journal of Molecular Biology	2008
18059443	Q-bio 2007: a watershed moment in modern biology.	Molecular Systems Biology	2007
17925356	Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism.	Annals of the New York Academy of Sciences	2007
18053142	Domain motions of Argonaute, the catalytic engine of RNA interference.	BMC Bioinformatics	2007
16513135	Interactions in native binding sites cause a large change in protein dynamics.	Journal of Molecular Biology	2006
16384030	Allostery in a coarse-grained model of protein dynamics.	Physical Review Letters	2005
15822100	Quantifying allosteric effects in proteins.	Proteins: Structure, Function and Bioinformatics	2005