Daniel Sindhikara
Daniel Sindhikara
Principal Scientist I, Schrodinger LLC
Verified email at schrodinger.com - Homepage
TitleCited byYear
Exchange frequency in replica exchange molecular dynamics
D Sindhikara, Y Meng, AE Roitberg
The Journal of chemical physics 128 (2), 01B609, 2008
1322008
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
1122009
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
992010
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
682012
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
662013
Analysis of biomolecular solvation sites by 3D-RISM theory
DJ Sindhikara, F Hirata
The Journal of Physical Chemistry B 117 (22), 6718-6723, 2013
522013
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
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
282017
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
242016
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
232016
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
162009
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
122017
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
92015
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
52011
High throughput evaluation of macrocyclization strategies for conformer stabilization
D Sindhikara, K Borrelli
Scientific reports 8 (1), 6585, 2018
42018
Analysis of Biomolecular Solvation Sites by the 3D-RISM Theory
F Hirata, DJ Sindhikara
US Patent App. 14/781,539, 2016
12016
Cyclization, docking, and sampling macrocycles with prime
D Sindhikara, T Day, K Borrelli
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 253, 2017
2017
Solving the macrocycle problem in silico
D Sindhikara, T Day, K Borrelli
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 252, 2016
2016
Leveraging fast, accurate macrocycle sampling for design and optimization
D Sindhikara, T Day, K Borrelli
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 250, 2015
2015
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Articles 1–20