Dan Sindhikara

1.7k total citations
26 papers, 1.2k citations indexed

About

Dan Sindhikara is a scholar working on Molecular Biology, Computational Theory and Mathematics and Atomic and Molecular Physics, and Optics. According to data from OpenAlex, Dan Sindhikara has authored 26 papers receiving a total of 1.2k indexed citations (citations by other indexed papers that have themselves been cited), including 23 papers in Molecular Biology, 8 papers in Computational Theory and Mathematics and 5 papers in Atomic and Molecular Physics, and Optics. Recurrent topics in Dan Sindhikara's work include Protein Structure and Dynamics (12 papers), Computational Drug Discovery Methods (8 papers) and Chemical Synthesis and Analysis (6 papers). Dan Sindhikara is often cited by papers focused on Protein Structure and Dynamics (12 papers), Computational Drug Discovery Methods (8 papers) and Chemical Synthesis and Analysis (6 papers). Dan Sindhikara collaborates with scholars based in United States, Japan and Germany. Dan Sindhikara's co-authors include Adrián E. Roitberg, Fumio Hirata, Norio Yoshida, Seonah Kim, Arthur F. Voter, Yilin Meng, Daniel J. Emerson, Ken Borrelli, Danielle M. Schultz and Susan L. Zultanski and has published in prestigious journals such as The Journal of Chemical Physics, Journal of Molecular Biology and The Journal of Physical Chemistry B.

In The Last Decade

Dan Sindhikara

25 papers receiving 1.2k citations

Peers

Dan Sindhikara
Hironori Kokubo Japan
Changge Ji China
Angela N. Migues United States
Kellon Belfon United States
John D. Bickel United States
Boris Aguilar United States
Tom Young United States
Benjamin D. Madej United States
Johan Ulander Sweden
Hironori Kokubo Japan
Dan Sindhikara
Citations per year, relative to Dan Sindhikara Dan Sindhikara (= 1×) peers Hironori Kokubo

Countries citing papers authored by Dan Sindhikara

Since Specialization
Citations

This map shows the geographic impact of Dan Sindhikara's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Dan Sindhikara with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Dan Sindhikara more than expected).

Fields of papers citing papers by Dan Sindhikara

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Dan Sindhikara. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Dan Sindhikara. The network helps show where Dan Sindhikara may publish in the future.

Co-authorship network of co-authors of Dan Sindhikara

This figure shows the co-authorship network connecting the top 25 collaborators of Dan Sindhikara. A scholar is included among the top collaborators of Dan Sindhikara based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Dan Sindhikara. Dan Sindhikara is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Dykstra, Ryan & Dan Sindhikara. (2025). Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics. Journal of Chemical Information and Modeling. 65(3). 1585–1604.
2.
Maini, Rumit, Christopher J. Hipolito, Lisa A. Vasicek, et al.. (2024). Analysis and Prediction of Chymotrypsin Substrate Preferences through Large Data Acquisition with Target‐Free mRNA Display. ChemBioChem. 26(3). e202400760–e202400760. 1 indexed citations
3.
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5.
Paulsen, Janet L., Haoyu S. Yu, Dan Sindhikara, et al.. (2020). Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. Journal of Chemical Information and Modeling. 60(7). 3489–3498. 14 indexed citations
6.
Sindhikara, Dan, et al.. (2020). Water Thermodynamics of Peptide Toxin Binding Sites on Ion Channels. Toxins. 12(10). 652–652. 3 indexed citations
7.
Sindhikara, Dan & Ken Borrelli. (2018). High throughput evaluation of macrocyclization strategies for conformer stabilization. Scientific Reports. 8(1). 6585–6585. 22 indexed citations
8.
Sindhikara, Dan, Steven A. Spronk, Tyler Day, et al.. (2017). Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling. Journal of Chemical Information and Modeling. 57(8). 1881–1894. 71 indexed citations
9.
Yu, Haoyu S., Yuqing Deng, Yujie Wu, et al.. (2017). Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. Journal of Chemical Theory and Computation. 13(12). 6290–6300. 41 indexed citations
10.
Rungrotmongkol, Thanyada, Dan Sindhikara, Saree Phongphanphanee, et al.. (2015). 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. Protein Science. 25(1). 147–158. 33 indexed citations
11.
Maeno, Akihiro, Dan Sindhikara, Fumio Hirata, et al.. (2015). Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme. Biophysical Journal. 108(1). 133–145. 32 indexed citations
12.
Sindhikara, Dan, et al.. (2014). Determination of the Formylglycinamide Ribonucleotide Amidotransferase Ammonia Pathway by Combining 3D-RISM Theory with Experiment. ACS Chemical Biology. 10(3). 698–704. 13 indexed citations
13.
Watanabe, Hiroshi, Kai Welke, Dan Sindhikara, Peter Hegemann, & Marcus Elstner. (2013). Towards an Understanding of Channelrhodopsin Function: Simulations Lead to Novel Insights of the Channel Mechanism. Journal of Molecular Biology. 425(10). 1795–1814. 58 indexed citations
14.
Sindhikara, Dan & Fumio Hirata. (2013). Analysis of Biomolecular Solvation Sites by 3D-RISM Theory. The Journal of Physical Chemistry B. 117(22). 6718–6723. 80 indexed citations
15.
Sindhikara, Dan, Norio Yoshida, & Fumio Hirata. (2012). Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase. Journal of Computational Chemistry. 33(18). 1536–1543. 123 indexed citations
16.
Sindhikara, Dan. (2012). Modular reweighting software for statistical mechanical analysis of biased equilibrium data. Computer Physics Communications. 183(7). 1560–1561. 1 indexed citations
17.
Sindhikara, Dan, Norio Yoshida, Mikio Kataoka, & Fumio Hirata. (2011). Solvent penetration in photoactive yellow protein R52Q mutant: A theoretical study. Journal of Molecular Liquids. 164(1-2). 120–122. 6 indexed citations
18.
Sindhikara, Dan, Daniel J. Emerson, & Adrián E. Roitberg. (2010). Exchange Often and Properly in Replica Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 6(9). 2804–2808. 104 indexed citations
19.
Sindhikara, Dan, Adrián E. Roitberg, & Kenneth M. Merz. (2009). Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations. Biochemistry. 48(50). 12024–12033. 13 indexed citations
20.
Sindhikara, Dan, Seonah Kim, Arthur F. Voter, & Adrián E. Roitberg. (2009). Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules. Journal of Chemical Theory and Computation. 5(6). 1624–1631. 185 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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