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D

David Ryan Koes

department of computational and systems biology

31H指数
169论文数
8.4K被引数
收录论文 53
发表时间
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FlowMol3: Flow Matching for 3D De Novo Small-Molecule GenerationFlowMol3：用于3D从头小分子生成的流匹配
errDigital Discovery
IF5.6
err2026-04-08
err0
errOAAI
errIan Dunn; David Ryan Koes
err分享
err收藏
Small molecule intervention of actin-binding protein profilin1 reduces tumor angiogenesis in renal cell carcinomaprofilin1这种肌动蛋白结合蛋白的小分子干预可降低肾细胞癌中的肿瘤血管生成。
errJournal of Biological Chemistry
IF3.9
err2025-12-11
err0
errOAAI
errDavid Gau; Pooja Chawla; Kexin Xu; Niharika Welling; Jacob Antonello; Caroline Consoli; Monica Wei; Sara Zdancewicz; Michael DaSilva; Chris Varghese; Paul Francoeur; Haibin Shi; Xucai Chen; Anurag Paranjape; Flordeliza Villanueva; Thomas E. Smithgall; Andrew VanDemark; David R. Koes; Donna M. Huryn; Partha Roy
err分享
err收藏
NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinityNEMO招募在单个细胞因子-受体复合物中显示出量子化动力学，且与配体亲和力无关
errCell Reports
IF6.9
err2025-12-02
err0
errOAAI
errA. Hyun Kim; Benjamin Krummenacher; Jason Yeung; David R. Koes; Robin E.C. Lee
err分享
err收藏
How evolution shaped the structure of steroidogenic cytochrome P450 11A进化如何塑造了类固醇生成细胞色素P450 11A的结构
errJournal of Inorganic Biochemistry
IF3.2
err2025-10-09
err0
errOAAI
errBrisa Caroline Alves Chagas; Bjoern Brixius; Pang Che Wang; Somayeh Pirhadi; Ozha Aziz; David R. Koes; Elizabeth M.J. Gillam; Rita Bernhardt; Simone Brixius-Anderko
err分享
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GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule GenerationGEOM-Drugs 再探：迈向更化学精确的 3D 分子生成基准
errDigital Discovery
IF5.6
err2025-10-03
err0
errOAAI
errFilipp Nikitin; Ian Dunn; David Ryan Koes; Olexandr Isayev
err分享
err收藏
Functional studies on the cytochrome P450 splice variants CYP4F3A and CYP4F3B unveil the basis for their distinct physiological functions关于细胞色素P450剪接变体CYP4F3A和CYP4F3B的功能研究表明，其独特的生理功能基础已被揭示。
errDrug Metabolism and Disposition
IF4
err2025-09-29
err0
errOAAI
errBrisa Caroline Alves Chagas; Bjoern Brixius; Somayeh Pirhadi; Adriana Mirtchev; Sutapa Ray; David R. Koes; Simone Brixius-Anderko
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PharmacoForge: pharmacophore generation with diffusion modelsPharmacoForge: 基于扩散模型的药效基生成
errFrontiers in Bioinformatics
IF3.9
err2025-09-27
err0
errOAAI
errEmma L. Flynn; Riya Shah ; Ian Dunn ; Rishal Aggarwal ; David Ryan Koes 
err分享
err收藏
Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions滑动窗口交互语法（SWING）：一种用于肽和蛋白质交互的广义交互语言模型
errNature Methods
IF32.1
err2025-07-28
err0
errOAAI
errJane C. Siwek; Alisa A. Omelchenko; Prabal Chhibbar; Sanya Arshad; AnnaElaine Rosengart; Iliyan Nazarali; Akash Patel; Kiran Nazarali; Javad Rahimikollu; Jeremy S. Tilstra; Mark J. Shlomchik; David R. Koes; Alok V. Joglekar; Jishnu Das
err分享
err收藏
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13CACHE挑战赛#2：靶向SARS-CoV-2解旋酶Nsp13的RNA位点
errJournal of Chemical Information and Modeling
IF5.3
err2025-06-20
err0
PREAI
errOleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar E. A. Arce; Roly J. Armstrong; Cheryl Arrowsmith; Kelly E. Bachta; Hartmut Beck; Denes Berta; Mateusz K. Bieniek; Vincent Blay; Albina Bolotokova; Philip E. Bourne; Marko Breznik; Peter J. Brown; Aaron D. G. Campbell; Emanuele Carosati; Irene Chau; Daniel J. Cole; Ben Cree; Wim Dehaen; Katrin Denzinger; Karina dos Santos Machado; Ian Dunn; Prasannavenkatesh Durai; Kristina Edfeldt; Aled Edwards; Darren Fayne; Daniel Felfoldi; Kallie Friston; Pegah Ghiabi; Elisa Gibson; Judith Günther; Anders Gunnarsson; Alexander Hillisch; Douglas R. Houston; Jan Halborg Jensen; Rachel J. Harding; Kate S. Harris; Laurent Hoffer; Anders Hogner; Joshua T. Horton; Scott Houliston; Judd F. Hultquist; Ashley Hutchinson; John J. Irwin; Marko Jukič; Shubhangi Kandwal; Andrea Karlova; Vittorio L. Katis; Ryan P. Kich; Dmitri Kireev; David Koes; Nicole L. Inniss; Uta Lessel; Sijie Liu; Peter Loppnau; Wei Lu; Sam Martino; Miles McGibbon; Jens Meiler; Akhila Mettu; Sam Money-Kyrle; Rocco Moretti; Yurii S. Moroz; Charuvaka Muvva; Joseph A. Newman; Leon Obendorf; Brooks Paige; Amit Pandit; Keunwan Park; Sumera Perveen; Rachael Pirie; Gennady Poda; Mykola Protopopov; Vera Pütter; Federico Ricci; Natalie J. Roper; Edina Rosta; Margarita Rzhetskaya; Yogesh Sabnis; Karla J. F. Satchell; Frederico Schmitt Kremer; Thomas Scott; Almagul Seitova; Casper Steinmann; Valerij Talagayev; Olga O. Tarkhanova; Natalie J. Tatum; Dakota Treleaven; Adriano Velasque Werhli; W. Patrick Walters; Xiaowen Wang; Jude Wells; Geoffrey Wells; Yvonne Westermaier; Gerhard Wolber; Lars Wortmann; Jixian Zhang; Zheng Zhao; Shuangjia Zheng; Matthieu Schapira
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GNINA 1.3: the next increment in molecular docking with deep learningGNINA 1.3: 深度学习分子对接的下一个增量
errJOURNAL OF CHEMINFORMATICS
IF5.7
err2025-03-02
err0
errOAAI
errMcnutt, Andrew T.; Li, Yanjing; Meli, Rocco; Aggarwal, Rishal; Koes, David Ryan
err分享
err收藏
PharmRL: pharmacophore elucidation with deep geometric reinforcement learningPharmRL：基于深度几何强化学习的药效团阐明
errBMC BIOLOGY
IF4.5
err2024-12-31
err3
errOAAI
errAggarwal, Rishal; Koes, David R.
err分享
err收藏
CACHE Challenge #1: Docking with GNINA Is All You Need缓存挑战 #1: 与GNINA对接是你所需要的
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-12-10
err1
errOAAI
errDunn, Ian; Pirhadi, Somayeh; Wang, Yao; Ravindran, Smmrithi; Concepcion, Carter; Koes, David Ryan
err分享
err收藏
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-11-05
err4
errOAAI
errLi, Fengling; Ackloo, Suzanne; Arrowsmith, Cheryl H.; Ban, Fuqiang; Barden, Christopher J.; Beck, Hartmut; Beranek, Jan; Berenger, Francois; Bolotokova, Albina; Bret, Guillaume; Breznik, Marko; Carosati, Emanuele; Chau, Irene; Chen, Yu; Cherkasov, Artem; Della Corte, Dennis; Denzinger, Katrin; Dong, Aiping; Draga, Sorin; Dunn, Ian; Edfeldt, Kristina; Edwards, Aled; Eguida, Merveille; Eisenhuth, Paul; Friedrich, Lukas; Fuerll, Alexander; Gardiner, Spencer S.; Gentile, Francesco; Ghiabi, Pegah; Gibson, Elisa; Glavatskikh, Marta; Gorgulla, Christoph; Guenther, Judith; Gunnarsson, Anders; Gusev, Filipp; Gutkin, Evgeny; Halabelian, Levon; Harding, Rachel J.; Hillisch, Alexander; Hoffer, Laurent; Hogner, Anders; Houliston, Scott; Irwin, John J.; Isayev, Olexandr; Ivanova, Aleksandra; Jacquemard, Celien; Jarrett, Austin J.; Jensen, Jan H.; Kireev, Dmitri; Kleber, Julian; Koby, S. Benjamin; Koes, David; Kumar, Ashutosh; Kurnikova, Maria G.; Kutlushina, Alina; Lessel, Uta; Liessmann, Fabian; Liu, Sijie; Lu, Wei; Meiler, Jens; Mettu, Akhila; Minibaeva, Guzel; Moretti, Rocco; Morris, Connor J.; Narangoda, Chamali; Noonan, Theresa; Obendorf, Leon; Pach, Szymon; Pandit, Amit; Perveen, Sumera; Poda, Gennady; Polishchuk, Pavel; Puls, Kristina; Puetter, Vera; Rognan, Didier; Roskams-Edris, Dylan; Schindler, Christina; Sindt, Francois; Spiwok, Vojtech; Steinmann, Casper; Stevens, Rick L.; Talagayev, Valerij; Tingey, Damon; Vu, Oanh; Walters, W. Patrick; Wang, Xiaowen; Wang, Zhenyu; Wolber, Gerhard; Wolf, Clemens Alexander; Wortmann, Lars; Zeng, Hong; Zepeda, Carlos A.; Zhang, Kam Y. J.; Zhang, Jixian; Zheng, Shuangjia; Schapira, Matthieu
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Interpreting forces as deep learning gradients improves quality of predicted protein structures
errBIOPHYSICAL JOURNAL
IF3.1
err2024-09-01
err1
errOAAI
errKing, Jonathan Edward; Koes, David Ryan
err分享
err收藏
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-06-07
err1
errOAAI
errBhatt, Roshni; Koes, David Ryan; Durrant, Jacob D.
err分享
err收藏
Actin-binding protein profilin1 is an important determinant of cellular phosphoinositide control
errJOURNAL OF BIOLOGICAL CHEMISTRY
IF3.9
err2024-01-01
err2
errOAAI
errRicci, Morgan M. C.; Orenberg, Andrew; Ohayon, Lee; Gau, David; Wills, Rachel C.; Bae, Yongho; Das, Tuhin; Koes, David; Hammond, Gerald R. V.; Roy, Partha
err分享
err收藏
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-12-19
err3
PREAI
errBrocidiacono, Michael; Francoeur, Paul; Aggarwal, Rishal; Popov, Konstantin I.; Koes, David Ryan; Tropsha, Alexander
err分享
err收藏
Open-ComBind: harnessing unlabeled data for improved binding pose prediction
errJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
IF3.1
err2023-12-08
err1
errOAAI
errMcNutt, Andrew T.; Koes, David Ryan
err分享
err收藏
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-11-24
err2
errOAAI
errFolmsbee, Dakota L.; Koes, David R.; Hutchison, Geoffrey R.
err分享
err收藏
Conformer Generation for Structure-Based Drug Design: How Many and How Good?
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-10-30
err15
errOAAI
errMcNutt, Andrew T.; Bisiriyu, Fatimah; Song, Sophia; Vyas, Ananya; Hutchison, Geoffrey R.; Koes, David Ryan
err分享
err收藏

研究方向

暂无研究方向
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P
Peter Wipf
H 指数: 96 · 论文数: 1.0K
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