🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Ameya Harmalkar

Johns Hopkins University

ORCID: 0000-0001-6863-9634
Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile
4.8Author DataRank

Indexed papers

3in pilot corpus
datarank_citation_only_1hop_v6· scope data_onlyMethodology
Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222
Top 9%
2.3DataRank
Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Papers

Driven by 13 papers — median percentile 89. Top paper: “Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment”.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222
Top 9%
2.3DataRank
Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26609
Top 11%
1.9DataRank
Top 11%81 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Utrecht University Repository (Utrecht University)(2023)10.22541/au.168888815.53957253/v1
Top 36%
0.540DataRank
Top 36%17 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Nature Communications(2021)10.1038/s41467-021-27222-7
N/A
0.500DataRank · unranked
27 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +45 more

Flexible protein–protein docking with a multitrack iterative transformer

Protein Science(2023)10.1002/pro.4862
N/A
0DataRank · unranked
32 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.29.547134
N/A
0DataRank · unranked
7 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange

eLife(2024)10.7554/elife.94029
N/A
0DataRank · unranked
6 citations

Sergey Lyskov, Jeffrey J. Gray, Ameya Harmalkar

Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange

eLife(2025)10.7554/elife.94029.3
N/A
0DataRank · unranked
15 citations

Sergey Lyskov, Jeffrey J. Gray, Ameya Harmalkar

Advances to tackle backbone flexibility in protein docking

Current Opinion in Structural Biology(2020)10.1016/j.sbi.2020.11.011
N/A
0DataRank · unranked
65 citations

Jeffrey J. Gray, Ameya Harmalkar

Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47–55

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70016
N/A
0DataRank · unranked
0 citations

Lee‐Shin Chu, Samuel W. Canner, Rituparna Samanta, Rahel Frick, Fátima A. Dávila-Hernández +4 more

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.04.438423
N/A
0DataRank · unranked
4 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +43 more

Induced fit with replica exchange improves protein complex structure prediction

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010124
N/A
0DataRank · unranked
16 citations

Sai Pooja Mahajan, Jeffrey J. Gray, Ameya Harmalkar

Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features

mAbs(2023)10.1080/19420862.2022.2163584
N/A
0DataRank · unranked
50 citations

Roshan Rao, Yuxuan Richard Xie, Jonas Honer, Wibke Deisting, Jonas Anlahr +12 more