83 citations · 238 across the 9 of their papers we have counts for
9 papers
DeepAtlas: a tool for effective manifold learning
Serena Hughes, Timothy Hamilton, Tom Kolokotrones +1
Manifold learning builds on the "manifold hypothesis," which posits that data in high-dimensional datasets are drawn from lower-dimensional manifolds. Current tools generate global…
Robust protein-protein interactions in crowded cellular environments
Eric Deeds, orr Ashenberg, Jaline Gerardine +1
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in prot…
A Structure-Centric View of Protein Evolution, Design and Adaptation
Eric J. Deeds, Eugene I. Shakhnovich
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of p…
High resolution protein folding with a transferable potential
Isaac A. Hubner, Eric J. Deeds, Eugene I. Shakhnovich
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different he…
The Emergence of Scaling in Sequence-based Physical Models of Protein Evolution
Eric J. Deeds, Eugene I. Shakhnovich
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships amon…
Protein Structure and Evolutionary History Determine Sequence Space Topology
Boris Shakhnovich, Eric Deeds, Charles Delisi +1
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of struc…