David Ryan Koes

Computer ScienceMaterials ScienceBiochemistry, Genetics and Molecular BiologyMedicine

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 31 papers. Top paper: “CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13”.

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c00535

N/A

0.292DataRank · unranked

6 citations

Madhushika Silva, Ayaz Ahmad, Oscar E. A. Arce, Roly J. Armstrong, Cheryl Arrowsmith +105 more

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13

ChemRxiv(2025)10.26434/chemrxiv-2025-8f0rq-v3

N/A

0.165DataRank · unranked

2 citations

Madhushika Silva, Abd Al‐Aziz A. Abu‐Saleh, Ayaz Ahmad, Jesus Antonio Alvarado-Huayhuaz, Oscar E. A. Arce +104 more

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13

ChemRxiv(2025)10.26434/chemrxiv-2025-8f0rq

N/A

0.150DataRank · unranked

1 citations

Madhushika Silva, Abd Al‐Aziz A. Abu‐Saleh, Ayaz Ahmad, Jesus Antonio Alvarado-Huayhuaz, Oscar E. A. Arce +104 more

Disruption of profilin1 function suppresses developmental and pathological retinal neovascularization

Journal of Biological Chemistry(2020)10.1074/jbc.ra120.012613

N/A

0DataRank · unranked

19 citations

Lucile Vignaud, Abigail Allen, Zhijian Guo, José‐Alain Sahel, David N. Boone +4 more

DeepFrag: a deep convolutional neural network for fragment-based lead optimization

Chemical Science(2021)10.1039/d1sc00163a

N/A

0DataRank · unranked

103 citations

David Ryan Koes, Jacob D. Durrant, Harrison Green

Virtual Screening with Gnina 1.0

Molecules(2021)10.3390/molecules26237369

N/A

0DataRank · unranked

51 citations

David Ryan Koes, Jocelyn Sunseri

Inhibition of ocular neovascularization by novel anti-angiogenic compound

Experimental Eye Research(2021)10.1016/j.exer.2021.108861

N/A

0DataRank · unranked

11 citations

Lucile Vignaud, Paul Francoeur, David Ryan Koes, Xavier Guillonneau, Partha Roy +1 more

Active Learning for Small Molecule pKa Regression; a Long Way To Go

ChemRxiv(2022)10.26434/chemrxiv-2022-8w1q0

N/A

0DataRank · unranked

4 citations

Daniel Peñaherrera, David Ryan Koes, Paul Francoeur

BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening

ChemRxiv(2022)10.26434/chemrxiv-2022-3qc9t-v2

N/A

0DataRank · unranked

3 citations

Paul Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha +1 more

Actin-binding protein profilin1 is an important determinant of cellular phosphoinositide control

Journal of Biological Chemistry(2023)10.1016/j.jbc.2023.105583

N/A

0DataRank · unranked

8 citations

Andrew Orenberg, Lee Ohayon, David Gau, Rachel C. Wills, Yongho Bae +5 more

Interpreting forces as deep learning gradients improves quality of predicted protein structures

Biophysical Journal(2023)10.1016/j.bpj.2023.12.011

N/A

0DataRank · unranked

4 citations

David Ryan Koes, Jonathan King

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure

PubMed(2023)10.48550/arxiv.2311.13466

N/A

0DataRank · unranked

3 citations

David Ryan Koes, Ian Dunn

PLANTAIN: Diffusion-inspired Pose Score Minimization for Fast and Accurate Molecular Docking

arXiv (Cornell University)(2023)10.48550/arxiv.2307.12090

N/A

0DataRank · unranked

2 citations

Konstantin I. Popov, David Ryan Koes, Alexander Tropsha, Michael Brocidiacono

Structure-Infused Protein Language Models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.13.571525

N/A

0DataRank · unranked

2 citations

David Ryan Koes, Daniel Peñaherrera

CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.18.562959

N/A

0DataRank · unranked

1 citations

David Ryan Koes, Jacob D. Durrant, Roshni Bhatt

BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening

ChemRxiv(2023)10.26434/chemrxiv-2022-3qc9t-v3

N/A

0DataRank · unranked

1 citations

Paul Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha +1 more

Conformer Generation for Structure Based Drug Design: How Many and How Good?

ChemRxiv(2023)10.26434/chemrxiv-2023-sl2d0

N/A

0DataRank · unranked

0 citations

Fatimah Bisiriyu, Sophia Song, Ananya Vyas, Geoffrey Hutchison, David Ryan Koes +1 more

Interpreting Molecular Dynamics Forces as Deep Learning Gradients Improves Quality Of Predicted Protein Structures

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.03.560775

N/A

0DataRank · unranked

0 citations

David Ryan Koes, Jonathan King

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c01267

N/A

0DataRank · unranked

26 citations

Suzanne Ackloo, C.H. Arrowsmith, Fuqiang Ban, Christopher Barden, Hartmut Beck +91 more

PharmRL: pharmacophore elucidation with deep geometric reinforcement learning

BMC Biology(2024)10.1186/s12915-024-02096-5

N/A

0DataRank · unranked

8 citations

David Ryan Koes, Rishal Aggarwal

CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson’s Disease associated protein

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.18.603797

N/A

0DataRank · unranked

5 citations

Suzanne Ackloo, C.H. Arrowsmith, Fuqiang Ban, Christopher Barden, Hartmut Beck +90 more

PharmRL: Pharmacophore elucidation with Deep Geometric Reinforcement Learning

Research Square(2024)10.21203/rs.3.rs-5033986/v1

N/A

0DataRank · unranked

2 citations

David Ryan Koes, Rishal Aggarwal

Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation

PubMed(2024)10.48550/arxiv.2404.19739

N/A

0DataRank · unranked

1 citations

David Ryan Koes, Ian Dunn

GNINA 1.3: the next increment in molecular docking with deep learning

Journal of Cheminformatics(2025)10.1186/s13321-025-00973-x

N/A

0DataRank · unranked

112 citations

Yanjing Li, Rocco Meli, Rishal Aggarwal, David Ryan Koes, Andrew T. McNutt

Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions

Nature Methods(2025)10.1038/s41592-025-02723-1

N/A

0DataRank · unranked

17 citations

Alisa A. Omelchenko, Prabal Chhibbar, Sanya Arshad, AnnaElaine Rosengart, Iliyan Nazarali +9 more

Small molecule intervention of actin-binding protein profilin1 reduces tumor angiogenesis in renal cell carcinoma

Journal of Biological Chemistry(2025)10.1016/j.jbc.2025.111033

N/A

0DataRank · unranked

1 citations

Pooja Chawla, Kexin Xu, Niharika Welling, Jacob Antonello, Caroline Consoli +15 more

NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity

Cell Reports(2025)10.1016/j.celrep.2025.116637

N/A

0DataRank · unranked

1 citations

Benjamin Krummenacher, Jason Yeung, David Ryan Koes, Robin Lee, A Hyun Kim

Duvelisib is a novel NFAT inhibitor that mitigates adalimumab-induced immunogenicity

Frontiers in Pharmacology(2025)10.3389/fphar.2024.1397995

N/A

0DataRank · unranked

0 citations

Yuyin Wang, Keito Hoshitsuki, Katherine M. Eichinger, Sanjay Rathod, Yin Zhu +7 more

Interpretable adenylation domain specificity prediction using protein language models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.13.632878

N/A

0DataRank · unranked

0 citations

Andrew T. McNutt, Caleb N. Ellington, Krish Suraparaju, Nan Fang, Donghui Yan +8 more

NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.18.649561

N/A

0DataRank · unranked

0 citations

Benjamin Krummenacher, Jason Yeung, David Ryan Koes, Robin Lee, A Hyun Kim

PharmacoForge: Pharmacophore Generation with Diffusion Models

ChemRxiv(2025)10.26434/chemrxiv-2025-dz765

N/A

0DataRank · unranked

0 citations

Riya Shah, Ian Dunn, Rishal Aggarwal, David Ryan Koes, Emma Flynn