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Author Details

Willy Wriggers
Old Dominion University
1997
74
33
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37613363Streamlining Phantom Tomogram Generation Through Situs and TomoSim Integration.Microsc Microanal2023
37613638Appraisal of AlphaFold2-Predicted Models in Cryo-EM Map Interpretation.Microsc Microanal2023
37613398Tracing Randomly Oriented Filaments in Cryo-Electron Tomography Maps.Microsc Microanal2023
35892332Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms.Biomolecules2022
37485023Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB Discov2022
34660691Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis.Front Mol Biosci2021
37448648<i>TomoSim</i>: Simulation of Filamentous Cryo-Electron Tomograms.Proceedings (IEEE Int Conf Bioinformatics Biomed)2021
37465415Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm.Proceedings (IEEE Int Conf Bioinformatics Biomed)2021
32452204Faces of Contemporary CryoEM Information and Modeling.J Chem Inf Model2020
32216344Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps.J Chem Inf Model2020
31192591Frontiers in CryoEM Modeling.J Chem Inf Model2019
29641472Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.Molecules2018
30219048Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.BMC Struct Biol2018
27936925Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.J Comput Biol2017
28487858A Balanced Approach to Adaptive Probability Density Estimation.Front Mol Biosci2017
28487856Computing Spatiotemporal Heat Maps of Lipid Electropore Formation: A Statistical Approach.Front Mol Biosci2017
26851071Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.J Mol Biol2016
27169521Spatial Heat Maps from Fast Information Matching of Fast and Slow Degrees of Freedom: Application to Molecular Dynamics Simulations.J Phys Chem B2016
27280059Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix.Proceedings (IEEE Int Conf Bioinformatics Biomed)2015
26505203Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor.PLoS Comput Biol2015
26416532Numerical geometry of map and model assessment.J Struct Biol2015
22155667Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions.J Struct Biol2012
23066432Developing a denoising filter for electron microscopy and tomography data in the cloud.Biophys Rev2012
23066431Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing.Biophys Rev2012
22837754An assembly model of rift valley Fever virus.Front Microbiol2012
22505255Conventions and workflows for using Situs.Acta Crystallogr D Biol Crystallogr2012
22433493Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.J Struct Biol2012
22325770Outcome of the first electron microscopy validation task force meeting.Structure2012
20854911Matching structural densities from different biophysical origins with gain and bias.J Struct Biol2011
21078392Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.J Struct Biol2011
21275429Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization.Biochemistry2011
20174447Using Situs for the integration of multi-resolution structures.Biophys Rev2010
20947758Atomic-level characterization of the structural dynamics of proteins.Science2010
19708737Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.J Chem Phys2009
26631775Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.J Chem Theory Comput2009
18951904Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.J Mol Biol2008
18855436Coarse-graining protein structures with local multivariate features from molecular dynamics.J Phys Chem B2008
18757874Biomolecular pleiomorphism probed by spatial interpolation of coarse models.Bioinformatics2008
17207812Limulus polyphemus hemocyanin: 10 A cryo-EM structure, sequence analysis, molecular modelling and rigid-body fitting reveal the interfaces between the eight hexamers.J Mol Biol2007
17029847Multi-resolution anchor-point registration of biomolecular assemblies and their components.J Struct Biol2007
16700056Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules.Proteins2006
17176049Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations.Biochemistry2006
15880774Control of protein functional dynamics by peptide linkers.Biopolymers2005
19177656Direct observation of counterion organization in F-actin polyelectrolyte bundles.Eur Phys J E Soft Matter2005
16236526Fast rotational matching of single-particle images.J Struct Biol2005
14725756Spanning the length scales of biomolecular simulation.Structure2004
15390267Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering.Proteins2004
12853566Like-charge attraction between polyelectrolytes induced by counterion charge density waves.Proc Natl Acad Sci U S A2003
12876338Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom.Acta Crystallogr D Biol Crystallogr2003
12914698Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.Cell2003
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Collaborators

James Andrew McCammon
Co-authored papers 3
Yao Cong
University of Chinese Academy of Sciences
Co-authored papers 3
David E Shaw
Columbia University
Co-authored papers 2
Wah Chiu
Stanford University
Co-authored papers 2
Wen Jiang
Purdue University. Electronic address: .
Co-authored papers 2
Joachim Frank
Columbia University
Co-authored papers 2
Seth A Darst
The Rockefeller University
Co-authored papers 2
Edward H Egelman
University of Virginia
Co-authored papers 2
Vitold E Galkin
Eastern Virginia Medical School
Co-authored papers 2
Rommie E Amaro
University of California
Co-authored papers 2
Charles L Brooks
University of Michigan ann arbor
Co-authored papers 1
Alasdair C Steven
National Institutes of Health
Co-authored papers 1
Steven J Ludtke
Baylor College of Medicine
Co-authored papers 1
Bridget Carragher
Columbia University
Co-authored papers 1
Matthew L Baker
McGovern Medical School at the University of Texas Health Science Center
Co-authored papers 1
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 1
Huanwang Yang
The State University of New Jersey
Co-authored papers 1
Aivett Bilbao
Co-authored papers 1
Michael G Rossmann
Purdue University
Co-authored papers 1
Peter W Marks
Center for Biologics Evaluation and Research
Co-authored papers 1
Pawel A Penczek
The University of Texas, McGovern Medical School
Co-authored papers 1
Harel Weinstein
Institute for Computational Biomedicine
Co-authored papers 1
Rajendra K Agrawal
School of Public Health, University at Albany
Co-authored papers 1
Kenneth H Downing
Lawrence Berkeley National Laboratory
Co-authored papers 1
Helen M Berman
The State University of New Jersey
Co-authored papers 1
Manfred Auer
Southeast University
Co-authored papers 1
Richard Henderson
Medical Research Council
Co-authored papers 1
John D Westbrook
The State University of New Jersey
Co-authored papers 1
Nikolaus Grigorieff
RNA Therapeutics Institute, University of Massachusetts Chan Medical School
Co-authored papers 1
Zhen-Hong Zhou
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Release 1.2