Daniel Sindhikara
Daniel Sindhikara
Principal Scientist I, Schrodinger LLC
Verified email at schrodinger.com - Homepage
Title
Cited by
Cited by
Year
Exchange frequency in replica exchange molecular dynamics
D Sindhikara, Y Meng, AE Roitberg
The Journal of chemical physics 128 (2), 01B609, 2008
1342008
Bad seeds sprout perilous dynamics: stochastic thermostat induced trajectory synchronization in biomolecules
DJ Sindhikara, S Kim, AF Voter, AE Roitberg
Journal of Chemical Theory and Computation 5 (6), 1624-1631, 2009
1252009
Exchange often and properly in replica exchange molecular dynamics
DJ Sindhikara, DJ Emerson, AE Roitberg
Journal of Chemical Theory and Computation 6 (9), 2804-2808, 2010
1022010
Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase
DJ Sindhikara, N Yoshida, F Hirata
Journal of computational chemistry 33 (18), 1536-1543, 2012
872012
Towards an understanding of Channelrhodopsin function: Simulations lead to novel insights of the channel mechanism
HC Watanabe, K Welke, DJ Sindhikara, P Hegemann, M Elstner
Journal of Molecular Biology, 2013
702013
Analysis of biomolecular solvation sites by 3D-RISM theory
DJ Sindhikara, F Hirata
The Journal of Physical Chemistry B 117 (22), 6718-6723, 2013
602013
Improving accuracy, diversity, and speed with prime macrocycle conformational sampling
D Sindhikara, SA Spronk, T Day, K Borrelli, DL Cheney, SL Posy
Journal of Chemical Information and Modeling 57 (8), 1881-1894, 2017
392017
Cavity as a source of conformational fluctuation and high-energy state: High-pressure NMR study of a cavity-enlarged mutant of T4Lysozyme
A Maeno, D Sindhikara, F Hirata, R Otten, FW Dahlquist, S Yokoyama, ...
Biophysical journal 108 (1), 133-145, 2015
312015
A 3D‐RISM/RISM study of the oseltamivir binding efficiency with the wild‐type and resistance‐associated mutant forms of the viral influenza B neuraminidase
J Phanich, T Rungrotmongkol, D Sindhikara, S Phongphanphanee, ...
Protein Science 25 (1), 147-158, 2016
282016
Simple predictive models of passive membrane permeability incorporating size-dependent membrane-water partition
SSF Leung, D Sindhikara, MP Jacobson
Journal of chemical information and modeling 56 (5), 924-929, 2016
242016
Accurate and reliable prediction of the binding affinities of macrocycles to their protein targets
HS Yu, Y Deng, Y Wu, D Sindhikara, AR Rask, T Kimura, R Abel, L Wang
Journal of chemical theory and computation 13 (12), 6290-6300, 2017
182017
Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations
DJ Sindhikara, AE Roitberg, KM Merz Jr
Biochemistry 48 (50), 12024-12033, 2009
152009
Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment
AS Tanwar, DJ Sindhikara, F Hirata, R Anand
ACS Chemical Biology 10 (3), 698-704, 2015
132015
High throughput evaluation of macrocyclization strategies for conformer stabilization
D Sindhikara, K Borrelli
Scientific reports 8 (1), 1-8, 2018
82018
Solvent penetration in photoactive yellow protein R52Q mutant: A theoretical study
DJ Sindhikara, N Yoshida, M Kataoka, F Hirata
Journal of Molecular Liquids 164 (1-2), 120-122, 2011
82011
Modular reweighting software for statistical mechanical analysis of biased equilibrium data
DJ Sindhikara
Computer Physics Communications 182 (10), 2227-2231, 2011
62011
A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding
E Miller, R Murphy, D Sindhikara, K Borrelli, M Grisewood, F Ranalli, ...
ChemRxiv, 2020
12020
Analysis of biomolecular solvation sites by the 3d-rism theory
F Hirata, DJ Sindhikara
12014
Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis
JL Paulsen, HS Yu, D Sindhikara, L Wang, TC Appleby, AG Villaseņor, ...
Journal of Chemical Information and Modeling, 2020
2020
Cyclization, docking, and sampling macrocycles with prime
D Sindhikara, T Day, K Borrelli
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 253, 2017
2017
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Articles 1–20