Search Results - "Park, Hahnbeom"

Improved protein structure prediction using predicted interresidue orientations by Yang, Jianyi, Anishchenko, Ivan, Park, Hahnbeom, Peng, Zhenling, Ovchinnikov, Sergey, Baker, David

“…The prediction of interresidue contacts and distances from coevolutionary data using deep learning has considerably advanced protein structure prediction…”
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Improved protein structure refinement guided by deep learning based accuracy estimation by Hiranuma, Naozumi, Park, Hahnbeom, Baek, Minkyung, Anishchenko, Ivan, Dauparas, Justas, Baker, David

“…We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses…”
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Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking by Park, Hahnbeom, Zhou, Guangfeng, Baek, Minkyung, Baker, David, DiMaio, Frank

“…Accurate and rapid calculation of protein-small molecule interaction free energies is critical for computational drug discovery. Because of the large chemical…”
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Protein structure determination using metagenome sequence data by Ovchinnikov, Sergey, Park, Hahnbeom, Varghese, Neha, Huang, Po-Ssu, Pavlopoulos, Georgios A., Kim, David E., Kamisetty, Hetunandan, Kyrpides, Nikos C., Baker, David

“…Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We…”
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Accurate prediction of protein structures and interactions using a three-track neural network by 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

“…DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network…”
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GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions by Ko, Junsu, Park, Hahnbeom, Seok, Chaok

“…Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is…”
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Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules by Park, Hahnbeom, Bradley, Philip, Greisen, Per, Liu, Yuan, Mulligan, Vikram Khipple, Kim, David E, Baker, David, DiMaio, Frank

“…Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking have been parametrized using existing…”
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Protein structure prediction using Rosetta in CASP12 by Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., DiMaio, Frank, Baker, David

“…We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we…”
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design by 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

“…Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation…”
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Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination by Pavlovicz, Ryan E, Park, Hahnbeom, DiMaio, Frank, Singh, Mona, Wallner, Björn

“…Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that…”
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Protein homology model refinement by large-scale energy optimization by Park, Hahnbeom, Ovchinnikov, Sergey, Kim, David E., DiMaio, Frank, Baker, David

“…Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein…”
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Protein oligomer modeling guided by predicted interchain contacts in CASP14 by Baek, Minkyung, Anishchenko, Ivan, Park, Hahnbeom, Humphreys, Ian R., Baker, David

“…For CASP14, we developed deep learning‐based methods for predicting homo‐oligomeric and hetero‐oligomeric contacts and used them for oligomer modeling. To…”
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High-resolution protein–protein docking by global optimization: recent advances and future challenges by Park, Hahnbeom, Lee, Hasup, Seok, Chaok

“…•Various global optimization methods have been employed in protein–protein docking.•Current docking methods can predict only moderate conformational…”
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Large-scale determination of previously unsolved protein structures using evolutionary information by Ovchinnikov, Sergey, Kinch, Lisa, Park, Hahnbeom, Liao, Yuxing, Pei, Jimin, Kim, David E, Kamisetty, Hetunandan, Grishin, Nick V, Baker, David

“…The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific…”
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Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments by Park, Hahnbeom, Lee, Gyu Rie, Heo, Lim, Seok, Chaok

“…Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein…”
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High‐accuracy refinement using Rosetta in CASP13 by Park, Hahnbeom, Lee, Gyu Rie, Kim, David E., Anishchenko, Ivan, Cong, Qian, Baker, David

“…Because proteins generally fold to their lowest free energy states, energy‐guided refinement in principle should be able to systematically improve the quality…”
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Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family by 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

“…Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in…”
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An artificial intelligence accelerated virtual screening platform for drug discovery by 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

“…Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries…”
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Divergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasites by Falekun, Seyi, Sepulveda, Jaime, Jami-Alahmadi, Yasaman, Park, Hahnbeom, Wohlschlegel, James A, Sigala, Paul A

“…Most eukaryotic cells retain a mitochondrial fatty acid synthesis (FASII) pathway whose acyl carrier protein (mACP) and 4-phosphopantetheine (Ppant) prosthetic…”
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Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy by Frenz, Brandon, Lewis, Steven M, King, Indigo, DiMaio, Frank, Park, Hahnbeom, Song, Yifan

“…Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To…”
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