C
Chaya S. Rapp
Researcher at Yeshiva University
Publications - 13
Citations - 2813
Chaya S. Rapp is an academic researcher from Yeshiva University. The author has contributed to research in topics: Implicit solvation & Hydrogen bond. The author has an hindex of 12, co-authored 13 publications receiving 2328 citations. Previous affiliations of Chaya S. Rapp include University of California, San Francisco & Columbia University.
Papers
More filters
Journal ArticleDOI
A hierarchical approach to all-atom protein loop prediction.
Matthew P. Jacobson,David L. Pincus,Chaya S. Rapp,Tyler Day,Barry Honig,David E. Shaw,Richard A. Friesner +6 more
TL;DR: The overall results are the best reported to date, and the combination of an accurate all‐atom energy function, efficient methods for loop buildup and side‐chain optimization, and, especially for the longer loops, the hierarchical refinement protocol is attributed.
Journal ArticleDOI
Generalized Born Model Based on a Surface Integral Formulation
TL;DR: This paper derived a surface-area-based version of the generalized Born model (S-GB) as a well-defined approximation to the boundary element formulation of the Poisson−Boltzmann (PB) equation.
Journal ArticleDOI
Force Field Validation Using Protein Side Chain Prediction
TL;DR: In this article, the prediction of protein side chain conformations is used to evaluate the accuracy of force field parameters, and new torsional parameters have been reported for the OPLS-AA force field, which achieved substantially better accuracy with respect to high level gas-phase quantum chemical calculations.
Journal ArticleDOI
Strengths of hydrogen bonds involving phosphorylated amino acid side chains.
Daniel J. Mandell,Ilya Chorny,Eli S. Groban,Sergio Wong,Elisheva Levine,Chaya S. Rapp,Matthew P. Jacobson +6 more
TL;DR: The effect of phosphate protonation state on the strengths of the hydrogen bonds is remarkably subtle, with a more pronounced effect on pAsp than on pSer, and Arg is shown to be capable of substantially stronger salt bridges with phosphorylated side chains than Lys.
Journal ArticleDOI
Prediction of loop geometries using a generalized born model of solvation effects.
TL;DR: This work has carried out an extensive exploration of the possibility of predicting the structure of long loops in proteins, using an 8‐ and a 12‐residue loop in ribonuclease A as models, using the native X‐ray structure as a template.