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

Lydia E. Kavraki

Rice University

ORCID: 0000-0003-0699-8038

Computer ScienceEngineeringBiochemistry, Genetics and Molecular Biology

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 16 papers. Top paper: “HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy”.

HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy

JCO Clinical Cancer Informatics(2020)10.1200/cci.19.00123

N/A

0DataRank · unranked

24 citations

Jayvee R. Abella, Sarah Hall-Swan, Didier Devaurs, Anja Conev, Mark Moll +3 more

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins

Computers in Biology and Medicine(2021)10.1016/j.compbiomed.2021.104943

N/A

0DataRank · unranked

14 citations

Didier Devaurs, Maurício Rigo, Dinler A. Antunes, Lydia E. Kavraki, Geancarlo Zanatta +1 more

3pHLA-score improves structure-based peptide-HLA binding affinity prediction

Scientific Reports(2022)10.1038/s41598-022-14526-x

N/A

0DataRank · unranked

14 citations

Didier Devaurs, Maurício Rigo, Dinler A. Antunes, Lydia E. Kavraki, Anja Conev

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development

Frontiers in Immunology(2022)10.3389/fimmu.2022.931155

N/A

0DataRank · unranked

3 citations

Romanos Fasoulis, Anja Conev, Sarah Hall-Swan, Dinler A. Antunes, Lydia E. Kavraki +1 more

An end-to-end deep learning framework for translating mass spectra to de-novo molecules

Communications Chemistry(2023)10.1038/s42004-023-00932-3

N/A

0DataRank · unranked

61 citations

Vijil Chenthamarakshan, Payel Das, Lydia E. Kavraki, Eleni Litsa

HLAEquity: Examining biases in pan-allele peptide-HLA binding predictors

iScience(2023)10.1016/j.isci.2023.108613

N/A

0DataRank · unranked

14 citations

Romanos Fasoulis, Sarah Hall-Swan, Rodrigo da Silva Ferreira, Lydia E. Kavraki, Anja Conev

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

Briefings in Bioinformatics(2023)10.1093/bib/bbad242

N/A

0DataRank · unranked

23 citations

Maurício Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas +5 more

Transfer learning improves pMHC kinetic stability and immunogenicity predictions

ImmunoInformatics(2023)10.1016/j.immuno.2023.100030

N/A

0DataRank · unranked

10 citations

Maurício Rigo, Dinler A. Antunes, Γεώργιος Παλιούρας, Lydia E. Kavraki, Romanos Fasoulis

PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure

Frontiers in Immunology(2023)10.3389/fimmu.2023.1108303

N/A

0DataRank · unranked

3 citations

Jared K. Slone, Maurício Rigo, Dinler A. Antunes, Gregory Lizée, Lydia E. Kavraki +1 more

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence

(2023)10.1145/3584371.3612953

N/A

0DataRank · unranked

5 citations

Todd J. Treangen, Lydia E. Kavraki, Felix Quintana

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.24.538094

N/A

0DataRank · unranked

1 citations

Maurício Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas +5 more

APE-Gen2.0: Expanding Rapid Class I Peptide–Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c01667

N/A

0DataRank · unranked

13 citations

Maurício Rigo, Gregory Lizée, Dinler A. Antunes, Lydia E. Kavraki, Romanos Fasoulis

RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c01278

N/A

0DataRank · unranked

0 citations

Γεώργιος Παλιούρας, Lydia E. Kavraki, Romanos Fasoulis

STAG-LLM: Predicting TCR-pHLA binding with protein language models and computationally generated 3D structures

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.09.004

N/A

0DataRank · unranked

7 citations

Minying Zhang, Peixin Jiang, Amanda Kay Montoya, Emily Bontekoe, Barbara Nassif Rausseo +3 more

TCR-pMHC Binding Specificity Prediction From Structure Using Graph Neural Networks

IEEE Transactions on Computational Biology and Bioinformatics(2025)10.1109/tcbbio.2024.3504235

N/A

0DataRank · unranked

12 citations

Anja Conev, Maurício Rigo, Alexandre Reuben, Lydia E. Kavraki, Jared K. Slone

DINC-ensemble: A web server for docking large ligands incrementally to an ensemble of receptor conformations

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169163

N/A

0DataRank · unranked

5 citations

Jing Chen, Lydia E. Kavraki, Anja Conev