Publications by authors named "Bruce R Donald"

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Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.
Allen C McBride, Feng Yu, Edward H Cheng, Aulane Mpouli, Aimee C Soe, Bruce R Donald

Proteins· January 2026

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* (Convex Closure *): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders.
Henry Childs, Allen C McBride, Bruce R Donald

bioRxiv· November 2025

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Predicting pose distribution of protein domains connected by flexible linkers is an unsolved problem.
Allen C McBride, Feng Yu, Edward H Cheng, Aulane Mpouli, Aimee C Soe, Bruce R Donald

bioRxiv· September 2025

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Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.
Yuxi Long, Bruce R Donald

PLoS Comput Biol· June 2025

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Has AlphaFold 3 Solved the Protein Folding Problem for D-Peptides?
Henry Childs, Pei Zhou, Bruce R Donald

bioRxiv· March 2025

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Predicting Affinity Through Homology (PATH): Interpretable Binding Affinity Prediction with Persistent Homology.
Yuxi Long, Bruce R Donald

bioRxiv· October 2024

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Protocol for Designing Noncanonical Peptide Binders in OSPREY.
Henry Childs, Nathan Guerin, Pei Zhou, Bruce R Donald

J Comput Biol· October 2024

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DexDesign: A new OSPREY-based algorithm for designing D-peptide inhibitors.
Nathan Guerin, Henry Childs, Pei Zhou, Bruce R Donald

bioRxiv· February 2024

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DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors.
Nathan Guerin, Henry Childs, Pei Zhou, Bruce R Donald

Protein Eng Des Sel· January 2024

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Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from and targeting LptA.
Kelly Huynh, Amanuel Kibrom, Bruce R Donald, Pei Zhou

J Struct Biol X· December 2023

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Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design.
Graham T Holt, Jason Gorman, Siyu Wang, Anna U Lowegard, Baoshan Zhang, Bruce R Donald

Cell Rep· July 2023

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Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions.
Valentina Kugler, Andreas Lieb, Nathan Guerin, Bruce R Donald, Eduard Stefan

Commun Biol· July 2023

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Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR.
Nathan Guerin, Teresa Kaserer, Bruce R Donald

STAR Protoc· April 2023

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RESISTOR: A New OSPREY Module to Predict Resistance Mutations.
Nathan Guerin, Teresa Kaserer, Bruce R Donald

J Comput Biol· December 2022

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Resistor: An algorithm for predicting resistance mutations via Pareto optimization over multistate protein design and mutational signatures.
Nathan Guerin, Andreas Feichtner, Eduard Stefan, Teresa Kaserer, Bruce R Donald

Cell Syst· October 2022

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Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.
Siyu Wang, Stephanie M Reeve, Graham T Holt, Adegoke A Ojewole, Marcel S Frenkel, Bruce R Donald

PLoS Comput Biol· February 2022

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Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface.
Anna U Lowegard, Marcel S Frenkel, Graham T Holt, Jonathan D Jou, Adegoke A Ojewole, Bruce R Donald

PLoS Comput Biol· June 2020

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Minimization-Aware Recursive A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape.
Jonathan D Jou, Graham T Holt, Anna U Lowegard, Bruce R Donald

J Comput Biol· April 2020

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Computational Analysis of Energy Landscapes Reveals Dynamic Features That Contribute to Binding of Inhibitors to CFTR-Associated Ligand.
Graham T Holt, Jonathan D Jou, Nicholas P Gill, Anna U Lowegard, Jeffrey W Martin, Bruce R Donald

J Phys Chem B· December 2019

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Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin Resistant .
Stephanie M Reeve, Debjani Si, Jolanta Krucinska, Yongzhao Yan, Kishore Viswanathan, Bruce R Donald

ACS Infect Dis· November 2019

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Protein Design by Provable Algorithms.
Mark A Hallen, Bruce R Donald

Commun ACM· October 2019

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OSPREY 3.0: Open-source protein redesign for you, with powerful new features.
Mark A Hallen, Jeffrey W Martin, Adegoke Ojewole, Jonathan D Jou, Anna U Lowegard, Bruce R Donald

J Comput Chem· November 2018

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Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics.
Yang Qi, Jeffrey W Martin, Adam W Barb, François Thélot, Anthony K Yan, Bruce R Donald

J Mol Biol· September 2018

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BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces.
Adegoke A Ojewole, Jonathan D Jou, Vance G Fowler, Bruce R Donald

J Comput Biol· July 2018

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CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.
Mark A Hallen, Bruce R Donald

Bioinformatics· July 2017

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