A. Watkins

发表

Accurate de novo design of hyperstable constrained peptides

David Baker, James M. Olson, Thomas Szyperski, 2016, Nature.

RNA 3D modeling with FARFAR2, online

Rhiju Das, Andrew Watkins, Rhiju Das, 2020, bioRxiv.

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.

Rhiju Das, A. Watkins, R. Rangan, 2020, Structure.

Blind prediction of noncanonical RNA structure at atomic accuracy

Luc Jaeger, Rhiju Das, Wipapat Kladwang, 2017, Science Advances.

Blind prediction of noncanonical RNA structure at atomic accuracy

Rhiju Das, W. Kladwang, L. Jaeger, 2017, bioRxiv.

Geometric deep learning of RNA structure

Andrew M. Watkins, Ron O. Dror, Rhiju Das, 2021, Science.

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites

Rhiju Das, J. Piccirilli, A. Watkins, 2019, Nature Communications.

Characterizing Ligand Interactions in Wild-type and Mutated HIV-1 Proteases

Leyte L. Winfield, A. Watkins, L. Winfield, 2014 .

Anatomy of β-Strands at Protein–Protein Interfaces

Andrew M. Watkins, Paramjit S. Arora, A. Watkins, 2014, ACS chemical biology.

Protein–Protein Interactions Mediated by Helical Tertiary Structure Motifs

A. Watkins, P. Arora, Michael G. Wuo, 2015, Journal of the American Chemical Society.

Computational design of mixed chirality peptide macrocycles with internal symmetry

Jason W. Labonte, Timothy W. Craven, Stephen A. Rettie, 2020, Protein science : a publication of the Protein Society.

Expanding the limits of the second genetic code with ribozymes

Jaime N. Coronado, Do Soon Kim, A. Ellington, 2019, Nature Communications.

Protein Domain Mimics as Modulators of Protein-Protein Interactions.

A. Watkins, P. Arora, N. Sawyer, 2017, Accounts of chemical research.

Rotamer libraries for the high-resolution design of β-amino acid foldamers

Timothy W. Craven, Richard Bonneau, P. D. Renfrew, 2016, bioRxiv.

Side-Chain Conformational Preferences Govern Protein-Protein Interactions.

Richard Bonneau, A. Watkins, P. Arora, 2016, Journal of the American Chemical Society.

Typical development workflow in the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Rotamer libraries for the high-resolution design of β-amino acid foldamers

Timothy W. Craven, Richard Bonneau, P. D. Renfrew, 2016, bioRxiv.

Values Statement: Equality and Inclusion in the RosettaCommons.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Commercial spin-off companies from the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Multi-segment preserving sampling for deep manifold sampler

Ji Won Park, A. Watkins, Daniel Berenberg, 2022, ArXiv.

Details of Remaining Collective Challenges.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Members of the RosettaCommons Consortium.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Growth in Rosetta PIs and conference attendees.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Correction to ‘Theoretical basis for stabilizing messenger RNA through secondary structure design’

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, Nucleic acids research.

Anchor Residues Govern Binding and Folding of an Intrinsically Disordered Domain.

A. Watkins, P. Arora, N. Sawyer, 2022, ACS chemical biology.

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Nathan C Frey, A. Regev, Payman Yadollahpour, 2022, bioRxiv.

Computationally-guided design and selection of ribosomal active site mutants with high activity

Ashty S. Karim, Do Soon Kim, Rhiju Das, 2022, bioRxiv.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design

Saeed Saremi, A. Watkins, V. Gligorijević, 2022, ArXiv.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

Deep learning models for predicting RNA degradation via dual crowdsourcing

Do Soon Kim, John J. Nicol, Rhiju Das, 2021, ArXiv.

Three-dimensional structure-guided evolution of a ribosome with tethered subunits

Do Soon Kim, Rhiju Das, V. Topkar, 2022, Nature Chemical Biology.

Community science designed ribosomes with beneficial phenotypes

Rhiju Das, Jeff Anderson-Lee, Eli Fisker, 2021, bioRxiv.

Effects of side chains in helix nucleation differ from helix propagation

N. Kallenbach, A. Watkins, P. Arora, 2014, Proceedings of the National Academy of Sciences.

FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds

Andrew M. Watkins, Rhiju Das, Rhiju Das, 2019, bioRxiv.

Computationally-guided design and selection of high performing ribosomal active site mutants

Ashty S. Karim, Do Soon Kim, Rhiju Das, 2022, Nucleic acids research.

Structure-based inhibition of protein-protein interactions.

Andrew M Watkins, Paramjit S Arora, A. Watkins, 2015, European journal of medicinal chemistry.

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Jason W. Labonte, Timothy W. Craven, Stephen A. Rettie, 2021, Proceedings of the National Academy of Sciences.

RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams

Rhiju Das, A. Watkins, 2021, NAR genomics and bioinformatics.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, bioRxiv.

Designing Peptides on a Quantum Computer

Brian D. Weitzner, Andrew M. Watkins, P. Douglas Renfrew, 2019, bioRxiv.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Nathan C Frey, A. Regev, Payman Yadollahpour, 2023, bioRxiv.

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

Andrew M. Watkins, Wah Chiu, Rhiju Das, 2020, Nature Methods.

Ribosolve: Rapid determination of three-dimensional RNA-only structures

Andrew M. Watkins, Wah Chiu, Kaiming Zhang, 2019, bioRxiv.

Theoretical basis for stabilizing messenger RNA through secondary structure design

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, Nucleic acids research.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Christian A. Choe, Do Soon Kim, John J. Nicol, 2022, Nature Communications.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.

Structure and ligand binding of the glutamine-II riboswitch

Lin Huang, Rhiju Das, Andrew M Watkins, 2019, Nucleic acids research.

Function-guided protein design by deep manifold sampling

A. Watkins, V. Gligorijević, Daniel Berenberg, 2021, bioRxiv.

Cryo-EM-guided engineering of T-box-tRNA modules with enhanced selectivity and sensitivity in translational regulation

Minghua Zhang, T. Henkin, A. Watkins, 2023, bioRxiv.

Using Rosetta for RNA homology modeling.

Rhiju Das, Andrew M Watkins, Ramya Rangan, 2019, Methods in enzymology.

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions.

Richard Bonneau, Andrew M Watkins, Paramjit S Arora, 2017, Methods in molecular biology.

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

W. Chiu, Rhiju Das, W. Kladwang, 2020, Nature Methods.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

Andrew Watkins, Krishna Praneeth Kilambi, P. Douglas Renfrew, 2013, PloS one.

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

M. Rynge, Rhiju Das, W. Kladwang, 2021, Nucleic acids research.

HippDB: a database of readily targeted helical protein-protein interactions

Andrew M. Watkins, Paramjit S. Arora, Christina M. Bergey, 2013, Bioinform..

Better together: Elements of successful scientific software development in a distributed collaborative community

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020, PLoS Comput. Biol..

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2023, bioRxiv.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

Predictive models of RNA degradation through dual crowdsourcing

Michele Tinti, Youhan Lee, Andrew M. Watkins, 2021, ArXiv.

Theoretical basis for stabilizing messenger RNA through secondary structure design

Christian A. Choe, Do Soon Kim, John J. Nicol, 2020, bioRxiv.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Protein Domain Mimics as Modulators of Protein-Protein Interactions.

A. Watkins, P. Arora, N. Sawyer, 2017, Accounts of chemical research.