| 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 | 199 | 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 | 167 | 2012 |
| Exchange frequency in replica exchange molecular dynamics D Sindhikara, Y Meng, AE Roitberg The Journal of chemical physics 128 (2), 2008 | 164 | 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 | 133 | 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 | 102 | 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 | 94 | 2013 |
| 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 | 82 | 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 | 79 | 2021 |
| 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 | 57 | 2016 |
| 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 | 47 | 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 | 46 | 2017 |
| 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 | 39 | 2015 |
| High throughput evaluation of macrocyclization strategies for conformer stabilization D Sindhikara, K Borrelli Scientific reports 8 (1), 6585, 2018 | 26 | 2018 |
| 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 | 22 | 2023 |
| 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 | 21 | 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 | 21 | 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 | 16 | 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 | 13 | 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 | 11 | 2021 |
| 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 | 10 | 2011 |
Norio YOSHIDAProfessor, Graduate School of Informatics, Nagoya UniversityVerified email at nagoya-u.jp
