Daniel J. Sindhikara

发表

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition

Siegfried S. F. Leung, Daniel J. Sindhikara, Matthew P. Jacobson, 2016, J. Chem. Inf. Model..

Modular reweighting software for statistical mechanical analysis of biased equilibrium data

Daniel J. Sindhikara, 2011, Comput. Phys. Commun..

Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase

Fumio Hirata, Daniel J. Sindhikara, Norio Yoshida, 2012, J. Comput. Chem..

Modular reweighting software for statistical mechanical analysis of biased equilibrium data

Daniel J. Sindhikara, 2011, Comput. Phys. Commun..

Exchange frequency in replica exchange molecular dynamics.

Daniel J. Sindhikara, A. Roitberg, Yilin Meng, 2008, The Journal of chemical physics.

High throughput evaluation of macrocyclization strategies for conformer stabilization

Daniel J. Sindhikara, K. Borrelli, 2018, Scientific Reports.

Analysis of biomolecular solvation sites by 3D-RISM theory.

Fumio Hirata, Daniel J. Sindhikara, Daniel J Sindhikara, 2013, The journal of physical chemistry. B.

Exchange Often and Properly in Replica Exchange Molecular Dynamics.

Daniel J. Sindhikara, Adrian E Roitberg, Daniel J Sindhikara, 2010, Journal of chemical theory and computation.

Solvent penetration in photoactive yellow protein R52Q mutant: A theoretical study

Norio Yoshida, Fumio Hirata, Daniel J. Sindhikara, 2011 .

Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.

Daniel J. Sindhikara, K. Merz, A. Roitberg, 2009, Biochemistry.

Water Thermodynamics of Peptide Toxin Binding Sites on Ion Channels

Daniel J. Sindhikara, K. Borrelli, Abba E. Leffler, 2020, Toxins.

Determination of the formylglycinamide ribonucleotide amidotransferase ammonia pathway by combining 3D-RISM theory with experiment.

Daniel J. Sindhikara, F. Hirata, R. Anand, 2015, ACS chemical biology.

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

Daniel J. Sindhikara, N. Yoshida, F. Hirata, 2016, Protein science : a publication of the Protein Society.

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding.

Daniel J. Sindhikara, Matthew J. Grisewood, Steven V. Jerome, 2020, Journal of chemical theory and computation.

Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins.

Daniel J. Sindhikara, G. Hessler, A. Evers, 2020, Journal of medicinal chemistry.

Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations

Daniel J. Sindhikara, M. Dimattia, Abba E. Leffler, 2021, Toxins.

Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations

Daniel J. Sindhikara, M. Dimattia, Hubert Li, 2021, Marine drugs.

High throughput evaluation of macrocyclization strategies for conformer stabilization

Daniel J. Sindhikara, K. Borrelli, 2018, Scientific Reports.

Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.

Fumio Hirata, Daniel J. Sindhikara, Frans A A Mulder, 2014, Biophysical journal.

Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism.

Kai Welke, Daniel J. Sindhikara, Marcus Elstner, 2013, Journal of molecular biology.

Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

Robert Abel, Lingle Wang, Daniel J. Sindhikara, 2017, Journal of chemical theory and computation.

Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis

Lingle Wang, Daniel J. Sindhikara, Janet L Paulsen, 2020, J. Chem. Inf. Model..

Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules.

Daniel J. Sindhikara, Arthur F Voter, Adrian E Roitberg, 2009, Journal of chemical theory and computation.

Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling

Daniel J. Sindhikara, Dan Sindhikara, Tyler Day, 2017, J. Chem. Inf. Model..

Beyond 20 in the 21st Century: Prospects and Challenges of Non-canonical Amino Acids in Peptide Drug Discovery.

Danielle M. Schultz, Daniel J. Sindhikara, S. L. Zultanski, 2023, ACS medicinal chemistry letters.

Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

Daniel J. Sindhikara, Haoyu S. Yu, Robert Abel, 2017, Journal of chemical theory and computation.

Exchange frequency in replica exchange molecular dynamics.

Daniel J. Sindhikara, A. Roitberg, Yilin Meng, 2008, The Journal of chemical physics.

Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling

Daniel J. Sindhikara, Shana L. Posy, Steven A. Spronk, 2017, Journal of Chemical Information and Modeling.

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding.

Daniel J. Sindhikara, S. L. Dixon, Matthew J. Grisewood, 2021, Journal of chemical theory and computation.