Andrew Leaver-Fay
Molecular Biology · 2007–2020
A researcher in the Science corpus: 19 papers; trusts 30 researchers and is trusted by 44 researchers here, as inferred from the citation graph.
Subfields
- Molecular Biology — 482 citations into it; #925 of 17,773 by trust here, #529 by citations
- Materials Chemistry — 268 citations into it; #716 of 11,513 by trust here, #1,121 by citations
- Computational Biology & Bioinformatics — 75 citations into it; #569 of 660 by trust here, #143 by citations
- Computational Theory and Mathematics — 66 citations into it
- Spectroscopy — 50 citations into it
- Organic Chemistry — 22 citations into it
- Artificial Intelligence — 7 citations into it
Whom Andrew Leaver-Fay trusts overall
Their strongest outbound trust, strongest first, inferred from their citations.
- David Baker
- Brian Kuhlman
- Roland L. Dunbrack
- James J. Havranek
- Rhiju Das
- Tanja Kortemme
- G. Dantas
- Hadley Wickham
- Feng Ding
- Jens Meiler
Who trusts Andrew Leaver-Fay overall
- David Baker
- Enrique Marcos
- Jianfu Zhou
- Hahnbeom Park
- Tanja Kortemme
- Rebecca F. Alford
- L. Nivón
- Julia Koehler Leman
- Brian D. Weitzner
- Jeffrey J. Gray
Papers from Andrew Leaver-Fay's perspective
Ordered by how strongly the researchers Andrew Leaver-Fay trusts endorse each paper. Same corpus, a different order for every researcher.
- Native protein sequences are close to optimal for their structures.
- Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.
- De novo protein design: fully automated sequence selection.
- Alternate states of proteins revealed by detailed energy landscape mapping
- Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.
- The Protein Data Bank.
- A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.
- A simple physical model for binding energy hot spots in protein–protein complexes
- Exploring protein native states and large‐scale conformational changes with a modified generalized born model (Proteins: Structure, Function, and Bioinformatics)
- Algorithms for minimization without derivatives
Their papers
- Predicting protein structures with a multiplayer online game (2010) — 1,393 citations
- Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011) — 1,780 citations
- MolProbity: all-atom contacts and structure validation for proteins and nucleic acids (2007) — 3,833 citations
- RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011) — 614 citations
- The Rosetta all-atom energy function for macromolecular modeling and design (2017) — 1,486 citations
- Role of conformational sampling in computing mutation-induced changes in protein structure and stability (2010) — 640 citations
- Structure guided forcefield optimization (2011) — 48 citations
- Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013) — 199 citations
- Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches (2011) — 68 citations
- Modeling Symmetric Macromolecular Structures in Rosetta3 (2011) — 210 citations
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020) — 783 citations
- De Novo Enzyme Design Using Rosetta3 (2011) — 337 citations
- A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta (2015) — 233 citations
- Computationally Designed Bispecific Antibodies Using Negative State Repertoires (2016) — 53 citations
- Maintaining solvent accessible surface area under rotamer substitution for protein design (2007) — 24 citations
- A Generic Program for Multistate Protein Design (2011) — 95 citations
- Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface (2014) — 248 citations
- Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta (2017) — 101 citations
- Better together: Elements of successful scientific software development in a distributed collaborative community (2020) — 37 citations