Daniel Sindhikara
Daniel Sindhikara
Principal Scientist, Merck
Potvrđena adresa e-pošte na - Početna stranica
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
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
Exchange frequency in replica exchange molecular dynamics
D Sindhikara, Y Meng, AE Roitberg
The Journal of chemical physics 128 (2), 2008
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
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
Analysis of biomolecular solvation sites by 3D-RISM theory
DJ Sindhikara, F Hirata
The Journal of Physical Chemistry B 117 (22), 6718-6723, 2013
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
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
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
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
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
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
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
High throughput evaluation of macrocyclization strategies for conformer stabilization
D Sindhikara, K Borrelli
Scientific reports 8 (1), 6585, 2018
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
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
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
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
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
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
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