Prati
Daniel Sindhikara
Daniel Sindhikara
Principal Scientist, Merck
Potvrđena adresa e-pošte na schrodinger.com - Početna stranica
Naslov
Citirano
Citirano
Godina
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
2052009
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
1672012
Exchange frequency in replica exchange molecular dynamics
D Sindhikara, Y Meng, AE Roitberg
The Journal of chemical physics 128 (2), 2008
1662008
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
1362010
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
1032017
Analysis of biomolecular solvation sites by 3D-RISM theory
DJ Sindhikara, F Hirata
The Journal of Physical Chemistry B 117 (22), 6718-6723, 2013
962013
Reliable and accurate solution to the induced fit docking problem for protein–ligand binding
EB Miller, RB Murphy, D Sindhikara, KW Borrelli, MJ Grisewood, F Ranalli, ...
Journal of Chemical Theory and Computation 17 (4), 2630-2639, 2021
842021
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
832013
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
612016
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
482017
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
462016
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
402015
Beyond 20 in the 21st century: prospects and challenges of non-canonical amino acids in peptide drug discovery
JL Hickey, D Sindhikara, SL Zultanski, DM Schultz
ACS Medicinal Chemistry Letters 14 (5), 557-565, 2023
342023
High throughput evaluation of macrocyclization strategies for conformer stabilization
D Sindhikara, K Borrelli
Scientific reports 8 (1), 6585, 2018
272018
Automated design of macrocycles for therapeutic applications: from small molecules to peptides and proteins
D Sindhikara, M Wagner, P Gkeka, S Güssregen, G Tiwari, G Hessler, ...
Journal of Medicinal Chemistry 63 (20), 12100-12115, 2020
212020
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
212009
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
162015
Evaluation of free energy calculations for the prioritization of macrocycle synthesis
JL Paulsen, HS Yu, D Sindhikara, L Wang, T Appleby, AG Villaseñor, ...
Journal of Chemical Information and Modeling 60 (7), 3489-3498, 2020
132020
Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations
D Katz, D Sindhikara, M DiMattia, AE Leffler
Toxins 13 (3), 193, 2021
122021
Potency-and selectivity-enhancing mutations of conotoxins for nicotinic acetylcholine receptors can be predicted using accurate free-energy calculations
D Katz, MA DiMattia, D Sindhikara, H Li, N Abraham, AE Leffler
Marine Drugs 19 (7), 367, 2021
102021
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