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Andrew Leaver-Fay
Researcher at University of North Carolina at Chapel Hill
Publications - 42
Citations - 11244
Andrew Leaver-Fay is an academic researcher from University of North Carolina at Chapel Hill. The author has contributed to research in topics: Chemistry & Computer science. The author has an hindex of 23, co-authored 38 publications receiving 9284 citations. Previous affiliations of Andrew Leaver-Fay include University of Washington & Duke University.
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Journal ArticleDOI
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Ian W. Davis,Andrew Leaver-Fay,Vincent B. Chen,Jeremy N. Block,Gary J. Kapral,Xueyi Wang,Laura Weston Murray,W. Bryan Arendall,Jack Snoeyink,Jane S. Richardson,David S. Richardson +10 more
TL;DR: MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes that provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics.
Book ChapterDOI
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Andrew Leaver-Fay,Michael D. Tyka,Steven M. Lewis,Oliver F. Lange,James Thompson,Ron Jacak,Kristian W. Kaufman,P. Douglas Renfrew,Colin A. Smith,William Sheffler,Ian W. Davis,Seth Cooper,Adrien Treuille,Daniel J. Mandell,Florian Richter,Yih-En Andrew Ban,Sarel J. Fleishman,Jacob E. Corn,David E. Kim,Sergey Lyskov,Monica Berrondo,Stuart Mentzer,Zoran Popović,James J. Havranek,John Karanicolas,Rhiju Das,Jens Meiler,Tanja Kortemme,Jeffrey J. Gray,Brian Kuhlman,David Baker,Philip Bradley +31 more
TL;DR: This chapter describes the requirements for the ROSETTA molecular modeling program's new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
Journal ArticleDOI
Predicting protein structures with a multiplayer online game
Seth Cooper,Firas Khatib,Adrien Treuille,Adrien Treuille,Janos Barbero,Jeehyung Lee,Michael Beenen,Andrew Leaver-Fay,Andrew Leaver-Fay,David Baker,David Baker,Zoran Popović,Foldit Players +12 more
TL;DR: Foldit is described, a multiplayer online game that engages non-scientists in solving hard prediction problems and shows that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues.
Journal ArticleDOI
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.
Rebecca F. Alford,Andrew Leaver-Fay,Jeliazko R. Jeliazkov,Matthew J. O’Meara,Frank DiMaio,Hahnbeom Park,Maxim V. Shapovalov,P. Douglas Renfrew,Vikram Khipple Mulligan,Kalli Kappel,Jason W. Labonte,Michael S. Pacella,Richard Bonneau,Philip Bradley,Roland L. Dunbrack,Rhiju Das,David Baker,Brian Kuhlman,Tanja Kortemme,Jeffrey J. Gray +19 more
TL;DR: This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15), and explains how to use Rosetta energies to identify and analyze the features of biomolecular models.
Journal ArticleDOI
Role of conformational sampling in computing mutation-induced changes in protein structure and stability.
TL;DR: This work explores the performance of protocols which sample an increasing diversity of conformations and finds that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that theresolution of the force field is matched to the resolution of the sampling method.