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P. Douglas Renfrew
P. Douglas Renfrew
Simons Foundation
Verified email at simonsfoundation.org - Homepage
Title
Cited by
Cited by
Year
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ...
Methods in enzymology 487, 545-574, 2011
17372011
The Rosetta all-atom energy function for macromolecular modeling and design
RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ...
Journal of chemical theory and computation 13 (6), 3031-3048, 2017
8742017
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ...
PloS one 8 (5), e63906, 2013
3422013
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
2972020
Structure-based protein function prediction using graph convolutional networks
V Gligorijević, PD Renfrew, T Kosciolek, JK Leman, D Berenberg, ...
Nature communications 12 (1), 3168, 2021
2072021
A preliminary survey of the peptoid folding landscape
GL Butterfoss, PD Renfrew, B Kuhlman, K Kirshenbaum, R Bonneau
Journal of the American Chemical Society 131 (46), 16798-16807, 2009
1252009
Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design
PD Renfrew, EJ Choi, R Bonneau, B Kuhlman
PLoS One 7 (3), e32637, 2012
1072012
Engineered coiled-coil protein microfibers
J Hume, J Sun, R Jacquet, PD Renfrew, JA Martin, R Bonneau, ...
Biomacromolecules 15 (10), 3503-3510, 2014
682014
Peptoid atropisomers
B Paul, GL Butterfoss, MG Boswell, PD Renfrew, FG Yeung, NH Shah, ...
Journal of the American Chemical Society 133 (28), 10910-10919, 2011
632011
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design
K Drew, PD Renfrew, TW Craven, GL Butterfoss, FC Chou, S Lyskov, ...
PLoS One 8 (7), e67051, 2013
622013
A rotamer library to enable modeling and design of peptoid foldamers
PD Renfrew, TW Craven, GL Butterfoss, K Kirshenbaum, R Bonneau
Journal of the American Chemical Society 136 (24), 8772-8782, 2014
502014
Thermoresponsive protein-engineered coiled-coil hydrogel for sustained small molecule release
LK Hill, M Meleties, P Katyal, X Xie, E Delgado-Fukushima, T Jihad, ...
Biomacromolecules 20 (9), 3340-3351, 2019
382019
Oligo(N‐alkoxy glycines): Trans substantiating peptoid conformations
PA Jordan, B Paul, GL Butterfoss, PD Renfrew, R Bonneau, ...
Peptide Science 96 (5), 617-626, 2011
312011
Designing peptides on a quantum computer
VK Mulligan, H Melo, HI Merritt, S Slocum, BD Weitzner, AM Watkins, ...
BioRxiv, 752485, 2019
302019
Using quantum mechanics to improve estimates of amino acid side chain rotamer energies
PD Renfrew, GL Butterfoss, B Kuhlman
Proteins: Structure, Function, and Bioinformatics 71 (4), 1637-1646, 2008
302008
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1
VK Mulligan, S Workman, T Sun, S Rettie, X Li, LJ Worrall, TW Craven, ...
Proceedings of the National Academy of Sciences 118 (12), e2012800118, 2021
272021
Better together: Elements of successful scientific software development in a distributed collaborative community
J Koehler Leman, BD Weitzner, PD Renfrew, SM Lewis, R Moretti, ...
PLoS computational biology 16 (5), e1007507, 2020
212020
Conformational preferences of peptide–peptoid hybrid oligomers
GL Butterfoss, K Drew, PD Renfrew, K Kirshenbaum, R Bonneau
Peptide Science 102 (5), 369-378, 2014
162014
Improved Stability and Half‐Life of Fluorinated Phosphotriesterase Using Rosetta
CY Yang, PD Renfrew, AJ Olsen, M Zhang, C Yuvienco, R Bonneau, ...
ChemBioChem 15 (12), 1761-1764, 2014
162014
Rotamer libraries for the high-resolution design of β-amino acid foldamers
AM Watkins, TW Craven, PD Renfrew, PS Arora, R Bonneau
Structure 25 (11), 1771-1780. e3, 2017
152017
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