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Srinivasa Murthy Gopal
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The power of coarse graining in biomolecular simulations
HI Ingólfsson, CA Lopez, JJ Uusitalo, DH de Jong, SM Gopal, X Periole, ...
Wiley Interdisciplinary Reviews: Computational Molecular Science 4 (3), 225-248, 2014
6042014
PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids that preserves near‐atomistic accuracy
SM Gopal, S Mukherjee, YM Cheng, M Feig
Proteins: Structure, Function, and Bioinformatics 78 (5), 1266-1281, 2010
1172010
PRIMO: a transferable coarse-grained force field for proteins
P Kar, SM Gopal, YM Cheng, A Predeus, M Feig
Journal of chemical theory and computation 9 (8), 3769-3788, 2013
1012013
Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations
AV Predeus, S Gul, SM Gopal, M Feig
The Journal of Physical Chemistry B 116 (29), 8610-8620, 2012
592012
A peptidic unconjugated GRP78/BiP ligand modulates the unfolded protein response and induces prostate cancer cell death
D Maddalo, A Neeb, K Jehle, K Schmitz, C Muhle-Goll, L Shatkina, ...
PloS one 7 (10), 2012
492012
Solvent effects on ligand binding to a serine protease
SM Gopal, F Klumpers, C Herrmann, LV Schäfer
Physical Chemistry Chemical Physics 19 (17), 10753-10766, 2017
352017
Transferring the PRIMO coarse-grained force field to the membrane environment: Simulations of membrane proteins and helix–helix association
P Kar, SM Gopal, YM Cheng, A Panahi, M Feig
Journal of chemical theory and computation 10 (8), 3459-3472, 2014
322014
Systematic evaluation of bundled SPC water for biomolecular simulations
SM Gopal, AB Kuhn, LV Schäfer
Physical Chemistry Chemical Physics 17 (13), 8393-8406, 2015
292015
Thermodynamic and kinetic characterization of transmembrane helix association
AB Pawar, SA Deshpande, SM Gopal, TA Wassenaar, CA Athale, ...
Physical Chemistry Chemical Physics 17 (2), 1390-1398, 2015
272015
Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields
SM Gopal, S Wingbermühle, J Schnatwinkel, S Juber, C Herrmann, ...
The Journal of Physical Chemistry B, 2020
262020
On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations
AB Kuhn, SM Gopal, LV Schäfer
Journal of chemical theory and computation 11 (9), 4460-4472, 2015
252015
De Novo Folding of the DNA‐Binding ATF‐2 Zinc Finger Motif in an All‐Atom Free‐Energy Forcefield
SM Gopal, W Wenzel
Angewandte Chemie 118 (46), 7890-7892, 2006
172006
All‐atom de novo protein folding with a scalable evolutionary algorithm
A Verma, SM Gopal, JS Oh, KH Lee, W Wenzel
Journal of computational chemistry 28 (16), 2552-2558, 2007
152007
α-Aminoisobutyric Acid-Stabilized Peptide SAMs with Low Nonspecific Protein Adsorption and Resistance against Marine Biofouling
CD Beyer, ML Reback, SM Gopal, KA Nolte, JA Finlay, AS Clare, ...
ACS Sustainable Chemistry & Engineering 8 (7), 2665-2671, 2020
132020
Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model
SM Gopal, K Klenin, W Wenzel
Proteins: Structure, Function, and Bioinformatics 77 (2), 330-341, 2009
112009
Massively Parallel All Atom Protein Folding in a Single Day.
A Verma, SM Gopal, A Schug, JS Oh, KV Klenin, KH Lee, W Wenzel
PARCO, 527-534, 2007
92007
Lipid-dependent Conformational Landscape of the ErbB2 Growth Factor Receptor Dimers
SM Gopal, AB Pawar, TA Wassenaar, D Sengupta
Chemistry and Physics of Lipids, 104911, 2020
82020
Molecular dynamics trajectory compression with a coarse-grained model
YM Cheng, SM Gopal, SM Law, M Feig
IEEE/ACM transactions on computational biology and bioinformatics 9 (2), 476-486, 2011
82011
Conformational Sampling in Structure Prediction and Refinement with Atomistic and Coarse-Grained Models
M Feig, SM Gopal, K Vadivel, A Stumpff-Kane
Multiscale Approaches to Protein Modeling, 85-109, 2011
72011
All-atom protein folding with free-energy forcefields
A Verma, SM Gopal, A Schug, T Herges, K Klenin, W Wenzel
Progress in molecular biology and translational science 83, 181-253, 2008
52008
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Articles 1–20