Publications


Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening
V. Tiwari and S.Viswanath
Scientific Reports, 2022


PrISM: precision for integrative structural models
V. Ullanat, N. Kasukurthi, S. Viswanath
Bioinformatics, 2022


Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination
S. Arvindekar, M. J. Jackman, J.K.K. Low, M.J. Landsberg, J.P. Mackay, S.Viswanath
Protein Science, 2022


A Framework for Stochastic Optimization of Parameters for Integrative Modeling of Macromolecular Assemblies
S. Pasani, S. Viswanath
Life (Spl. Issue on Computational Modeling of Kinetics in Biological Systems), 2021


Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure
D. Saltzberg, S. Viswanath, I. Echeverria, I.E. Chemmama, B. Webb, A. Sali
Protein Science, 2021
PDF Website


CM1-driven assembly and activation of Yeast γ-Tubulin Small Complex underlies microtubule nucleation
A. Brilot, A.S. Lyon, A. Zelter, S. Viswanath, A. Maxwell, R. Johnson, K.C. Yabut, M. MacCoss, E. Muller, A. Sali, T.N. Davis, D. A. Agard
eLife, 2021


Optimizing model representation for integrative structure determination of macromolecular assemblies
S. Viswanath and A. Sali
PNAS, 2019


Modeling biological complexes using Integrative Modeling Platform, Biomolecular Simulations Series
D. Saltzberg, C.H. Greenberg, S. Viswanath, I.E. Chemmama, B. Webb, R. Pellarin, I. Echeverria, A. Sali
Methods in Molecular Biology, 2019


Integrative structure modeling with the Integrative Modeling Platform
B. Webb, S. Viswanath, M. Bonomi, R. Pellarin, C.H. Greenberg, D. Saltzberg, A. Sali
Protein Science, 2018


Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures
S. Viswanath, I.E. Chemmama, P. Cimermancic, A. Sali
Biophysical Journal, 2017


The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.
S. Viswanath, M. Bonomi, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, E.G. Muller
Molecular Biology of the Cell, 2017


Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
M.F. Lensink, S. Velankar, …, S. Viswanath, R. Elber, …, (several authors), S.J. Wodak
Proteins, 2016
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Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization
S. Viswanath, L. Dominguez, L.S. Foster, J.E. Straub, R. Elber
Proteins, 2015
PDF Website


Architecture of the human and yeast general transcription and DNA repair factor TFIIH
J. Luo, P. Cimermancic, S. Viswanath, C. C. Ebmeier, B. Kim, M. Dehecq, V. Raman, C.H. Greenberg, R. Pellarin, A. Sali, D. Taatjes, S. Hahn, J. Ranish
Molecular Cell, 2015


DOCK/PIERR: web server for structure prediction of protein-protein complexes
S. Viswanath, D.V.S. Ravikant, R. Elber
Protein Structure Prediction, Methods in Molecular Biology, 2014
PDF Website Server


Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples
S. Viswanath, S.M. Kreuzer, A.E. Cardenas, R. Elber
The Journal of Chemical Physics, 2013
PDF Website


Improving ranking of models for protein complexes with side chain modeling and atomic potentials
S. Viswanath, D.V.S. Ravikant, R. Elber
Proteins, 2013