Improved protein structure refinement guided by deep learning based accuracy estimation
Hiranuma, Naozumi, Park, Hahnbeom, Baek, Minkyung, Anishchenko, Ivan, Dauparas, Justas, Baker, David
Published in Nature communications (26.02.2021)
Published in Nature communications (26.02.2021)
Get full text
Journal Article
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
Park, Hahnbeom, Zhou, Guangfeng, Baek, Minkyung, Baker, David, DiMaio, Frank
Published in Journal of chemical theory and computation (09.03.2021)
Published in Journal of chemical theory and computation (09.03.2021)
Get full text
Journal Article
Protein structure determination using metagenome sequence data
Ovchinnikov, Sergey, Park, Hahnbeom, Varghese, Neha, Huang, Po-Ssu, Pavlopoulos, Georgios A., Kim, David E., Kamisetty, Hetunandan, Kyrpides, Nikos C., Baker, David
Published in Science (American Association for the Advancement of Science) (20.01.2017)
Published in Science (American Association for the Advancement of Science) (20.01.2017)
Get full text
Journal Article
Accurate prediction of protein structures and interactions using a three-track neural network
Baek, Minkyung, DiMaio, Frank, Anishchenko, Ivan, Dauparas, Justas, Ovchinnikov, Sergey, Lee, Gyu Rie, Wang, Jue, Cong, Qian, Kinch, Lisa N, Schaeffer, R Dustin, Millán, Claudia, Park, Hahnbeom, Adams, Carson, Glassman, Caleb R, DeGiovanni, Andy, Pereira, Jose H, Rodrigues, Andria V, van Dijk, Alberdina A, Ebrecht, Ana C, Opperman, Diederik J, Sagmeister, Theo, Buhlheller, Christoph, Pavkov-Keller, Tea, Rathinaswamy, Manoj K, Dalwadi, Udit, Yip, Calvin K, Burke, John E, Garcia, K Christopher, Grishin, Nick V, Adams, Paul D, Read, Randy J, Baker, David
Published in Science (American Association for the Advancement of Science) (20.08.2021)
Published in Science (American Association for the Advancement of Science) (20.08.2021)
Get full text
Journal Article
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
Park, Hahnbeom, Bradley, Philip, Greisen, Per, Liu, Yuan, Mulligan, Vikram Khipple, Kim, David E, Baker, David, DiMaio, Frank
Published in Journal of chemical theory and computation (13.12.2016)
Published in Journal of chemical theory and computation (13.12.2016)
Get full text
Journal Article
Protein structure prediction using Rosetta in CASP12
Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., DiMaio, Frank, Baker, David
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
Get full text
Journal Article
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J
Published in Journal of chemical theory and computation (13.06.2017)
Published in Journal of chemical theory and computation (13.06.2017)
Get full text
Journal Article
Protein homology model refinement by large-scale energy optimization
Park, Hahnbeom, Ovchinnikov, Sergey, Kim, David E., DiMaio, Frank, Baker, David
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
Get full text
Journal Article
High-resolution protein–protein docking by global optimization: recent advances and future challenges
Park, Hahnbeom, Lee, Hasup, Seok, Chaok
Published in Current opinion in structural biology (01.12.2015)
Published in Current opinion in structural biology (01.12.2015)
Get full text
Journal Article
Large-scale determination of previously unsolved protein structures using evolutionary information
Ovchinnikov, Sergey, Kinch, Lisa, Park, Hahnbeom, Liao, Yuxing, Pei, Jimin, Kim, David E, Kamisetty, Hetunandan, Grishin, Nick V, Baker, David
Published in eLife (03.09.2015)
Published in eLife (03.09.2015)
Get full text
Journal Article
High‐accuracy refinement using Rosetta in CASP13
Park, Hahnbeom, Lee, Gyu Rie, Kim, David E., Anishchenko, Ivan, Cong, Qian, Baker, David
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
Published in Proteins, structure, function, and bioinformatics (01.12.2019)
Get full text
Journal Article
An artificial intelligence accelerated virtual screening platform for drug discovery
Zhou, Guangfeng, Rusnac, Domnita-Valeria, Park, Hahnbeom, Canzani, Daniele, Nguyen, Hai Minh, Stewart, Lance, Bush, Matthew F., Nguyen, Phuong Tran, Wulff, Heike, Yarov-Yarovoy, Vladimir, Zheng, Ning, DiMaio, Frank
Published in Nature communications (05.09.2024)
Published in Nature communications (05.09.2024)
Get full text
Journal Article
Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family
Choi, Chulwon, Bae, Jungnam, Kim, Seonghan, Lee, Seho, Kang, Hyunook, Kim, Jinuk, Bang, Injin, Kim, Kiheon, Huh, Won-Ki, Seok, Chaok, Park, Hahnbeom, Im, Wonpil, Choi, Hee-Jung
Published in Nature communications (07.12.2023)
Published in Nature communications (07.12.2023)
Get full text
Journal Article
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy
Frenz, Brandon, Lewis, Steven M, King, Indigo, DiMaio, Frank, Park, Hahnbeom, Song, Yifan
Published in Frontiers in bioengineering and biotechnology (08.10.2020)
Published in Frontiers in bioengineering and biotechnology (08.10.2020)
Get full text
Journal Article