Author

D. A. Rufa

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Biophysics· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

J. D. Chodera· 2 shared A. E. Roitberg· 1 shared H. E. Bruce Macdonald· 1 shared I. Pulido· 1 shared I. Zhang· 1 shared J. Fass· 1 shared K. Hauser· 1 shared L. E. Rosen· 1 shared

Activity by Year

2020-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBiophysics

J. D. Chodera

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

I. Zhang, D. A. Rufa, I. Pulido, M. M. Henry, L. E. Rosen, K. Hauser, S. Singh, J. D. Chodera

This study identifies sampling challenges in protein:protein binding free energy calculations and demonstrates how to overcome them using alchemical methods and long simulations.

bioRxiv · Mar 7, 2023Biophysics

Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials

D. A. Rufa, H. E. Bruce Macdonald, J. Fass, M. Wieder, P. B. Grinaway, A. E. Roitberg, O. Isayev, J. D. Chodera

This paper improves the accuracy of alchemical free energy calculations for protein-ligand binding by combining machine learning and molecular mechanics potentials, reducing errors from 0.97 to 0.47 kcal mol-1.

bioRxiv · Jul 29, 2020 · PreprintBiophysics