Rafael C. Bernardi

6.7k total citations · 1 hit paper
50 papers, 2.4k citations indexed

About

Rafael C. Bernardi is a scholar working on Molecular Biology, Atomic and Molecular Physics, and Optics and Materials Chemistry. According to data from OpenAlex, Rafael C. Bernardi has authored 50 papers receiving a total of 2.4k indexed citations (citations by other indexed papers that have themselves been cited), including 38 papers in Molecular Biology, 18 papers in Atomic and Molecular Physics, and Optics and 12 papers in Materials Chemistry. Recurrent topics in Rafael C. Bernardi's work include Protein Structure and Dynamics (17 papers), Force Microscopy Techniques and Applications (12 papers) and Enzyme Structure and Function (11 papers). Rafael C. Bernardi is often cited by papers focused on Protein Structure and Dynamics (17 papers), Force Microscopy Techniques and Applications (12 papers) and Enzyme Structure and Function (11 papers). Rafael C. Bernardi collaborates with scholars based in United States, Germany and Brazil. Rafael C. Bernardi's co-authors include Klaus Schulten, Marcelo C. R. Melo, Hermann E. Gaub, Till Rudack, Zaida Luthey‐Schulten, Lukas F. Milles, João V. Ribeiro, Boon Chong Goh, C. Keith Cassidy and John E. Stone and has published in prestigious journals such as Science, Proceedings of the National Academy of Sciences and Journal of the American Chemical Society.

In The Last Decade

Rafael C. Bernardi

48 papers receiving 2.4k citations

Hit Papers

1 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Enhanced sampling techniques in molecular dynamics simulations of biological systems

2014 523 citations Rafael C. Bernardi, Marcelo C. R. Melo et al. profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Rafael C. Bernardi United States	21	1.6k	620	416	224	207	50	2.4k
Naveen Michaud‐Agrawal United States	4	1.7k 1.1×	329 0.5×	438 1.1×	253 1.1×	143 0.7×	4	2.7k
Mitsunori Ikeguchi Japan	32	2.3k 1.5×	453 0.7×	654 1.6×	286 1.3×	163 0.8×	141	3.1k
André H. Juffer Finland	22	1.5k 1.0×	446 0.7×	392 0.9×	214 1.0×	199 1.0×	69	2.5k
Nilesh K. Banavali United States	23	2.3k 1.4×	307 0.5×	413 1.0×	209 0.9×	104 0.5×	53	2.9k
Nathalie Reuter Norway	34	2.1k 1.3×	409 0.7×	558 1.3×	105 0.5×	239 1.2×	94	3.3k
Christoph Klein United States	8	1.7k 1.1×	304 0.5×	576 1.4×	211 0.9×	118 0.6×	16	2.5k
Pratul K. Agarwal United States	29	2.3k 1.5×	495 0.8×	903 2.2×	251 1.1×	308 1.5×	100	3.4k
N. Krawetz United States	2	1.4k 0.9×	303 0.5×	392 0.9×	274 1.2×	137 0.7×	2	2.1k
Barry Isralewitz United States	11	1.4k 0.9×	882 1.4×	366 0.9×	222 1.0×	356 1.7×	14	2.2k
Pemra Doruker Türkiye	31	1.8k 1.2×	299 0.5×	1.0k 2.4×	254 1.1×	150 0.7×	76	2.7k

Countries citing papers authored by Rafael C. Bernardi

Since Specialization

Citations

This map shows the geographic impact of Rafael C. Bernardi'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 Rafael C. Bernardi with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Rafael C. Bernardi more than expected).

Fields of papers citing papers by Rafael C. Bernardi

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Rafael C. Bernardi. 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 Rafael C. Bernardi. The network helps show where Rafael C. Bernardi may publish in the future.

Co-authorship network of co-authors of Rafael C. Bernardi

This figure shows the co-authorship network connecting the top 25 collaborators of Rafael C. Bernardi. A scholar is included among the top collaborators of Rafael C. Bernardi 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 Rafael C. Bernardi. Rafael C. Bernardi is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Bernardi, Rafael C., et al.. (2025). Impact of Structural Relaxation on Protein–Protein Docking in Large Macromolecular Complexes. SHILAP Revista de lepidopterología. 4(4). 48–48.

Mathelié‐Guinlet, Marion, Diego E. B. Gomes, Zhiyong Zheng, et al.. (2025). Ultrastrong Staphylococcus aureus adhesion to human skin: Calcium as a key regulator of noncovalent interactions. Science Advances. 11(36). eadu7457–eadu7457. 2 indexed citations

Zhang, Qingrong, et al.. (2025). Probing SARS-CoV-2 membrane binding peptide via single-molecule AFM-based force spectroscopy. Nature Communications. 16(1). 6–6. 5 indexed citations

Gomes, Diego E. B., et al.. (2024). Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. Journal of the American Chemical Society. 146(34). 23842–23853. 13 indexed citations

Yang, Byeongseon, et al.. (2024). Engineering the Mechanical Stability of a Therapeutic Complex between Affibody and Programmed Death-Ligand 1 by Anchor Point Selection. ACS Nano. 18(46). 31912–31922. 2 indexed citations

Stone, John E., João V. Ribeiro, Jan Saam, et al.. (2023). VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. Journal of Chemical Information and Modeling. 63(15). 4664–4678. 45 indexed citations

Koehler, Melanie, Joshua D. Simpson, Diego E. B. Gomes, et al.. (2023). Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proceedings of the National Academy of Sciences. 120(21). e2220741120–e2220741120. 10 indexed citations

Melo, Marcelo C. R. & Rafael C. Bernardi. (2023). Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike. Biophysical Journal. 122(14). 2833–2840. 9 indexed citations

Bauer, Magnus S., Marcelo C. R. Melo, Thomas Nicolaus, et al.. (2023). Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern. Nature Nanotechnology. 19(3). 399–405. 14 indexed citations

10.

Melo, Marcelo C. R., Diego E. B. Gomes, & Rafael C. Bernardi. (2022). Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. Journal of the American Chemical Society. 145(1). 70–77. 15 indexed citations

11.

Bauer, Magnus S., Lukas F. Milles, Thomas Nicolaus, et al.. (2022). A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions. Proceedings of the National Academy of Sciences. 119(14). e2114397119–e2114397119. 39 indexed citations

12.

Cann, Isaac, Gabriel Vasconcelos Pereira, Ahmed M. Abdel-Hamid, et al.. (2020). Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Applied and Environmental Microbiology. 86(7). 17 indexed citations

13.

Milles, Lukas F., Klaus Schulten, Hermann E. Gaub, & Rafael C. Bernardi. (2018). Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science. 359(6383). 1527–1533. 164 indexed citations

14.

Milles, Lukas F., Rafael C. Bernardi, Klaus Schulten, & Hermann E. Gaub. (2018). Deconstructing the Single Molecule Mechanics of an Ultrastable Pathogen Adhesin. Biophysical Journal. 114(3). 386a–386a. 2 indexed citations

15.

Scheurer, Maximilian, Marc Siggel, Rafael C. Bernardi, et al.. (2018). PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations. Biophysical Journal. 114(3). 577–583. 103 indexed citations

16.

Ribeiro, João V., Rafael C. Bernardi, Till Rudack, et al.. (2016). QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts. Scientific Reports. 6(1). 26536–26536. 145 indexed citations

17.

Perilla, Juan R., Boon Chong Goh, C. Keith Cassidy, et al.. (2015). Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology. 31. 64–74. 309 indexed citations

18.

Schoeler, Constantin, Rafael C. Bernardi, Klara H. Malinowska, et al.. (2015). Mapping Mechanical Force Propagation through Biomolecular Complexes. Nano Letters. 15(11). 7370–7376. 71 indexed citations

19.

Melo, Marcelo C. R., Rafael C. Bernardi, & Pedro G. Pascutti. (2013). Large Scale Structure Sampling for Protein Fold Prediction using the Generalized Simulated Annealing. Biophysical Journal. 104(2). 228a–229a. 1 indexed citations

20.

Bernardi, Rafael C. & Pedro G. Pascutti. (2012). Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction. Journal of Chemical Theory and Computation. 8(7). 2197–2203. 15 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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