A
Andrey Krokhotin
Researcher at Howard Hughes Medical Institute
Publications - 23
Citations - 916
Andrey Krokhotin is an academic researcher from Howard Hughes Medical Institute. The author has contributed to research in topics: RNA & Chromatin. The author has an hindex of 10, co-authored 23 publications receiving 616 citations. Previous affiliations of Andrey Krokhotin include University of North Carolina at Chapel Hill & Stanford University.
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Journal ArticleDOI
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Zhichao Miao,Ryszard W. Adamiak,Marc Frédérick Blanchet,Michal J. Boniecki,Janusz M. Bujnicki,Janusz M. Bujnicki,Shi-Jie Chen,Clarence Yu Cheng,Grzegorz Chojnowski,Fang-Chieh Chou,Pablo Cordero,José Almeida Cruz,Adrian R. Ferré-D'Amaré,Rhiju Das,Feng Ding,Nikolay V. Dokholyan,Stanislaw Dunin-Horkawicz,Wipapat Kladwang,Andrey Krokhotin,Grzegorz Lach,Marcin Magnus,François Major,Thomas H. Mann,Benoît Masquida,Dorota Matelska,Mélanie Meyer,Alla Peselis,Mariusz Popenda,Katarzyna J. Purzycka,Alexander Serganov,Juliusz Stasiewicz,Marta Szachniuk,Arpit Tandon,Siqi Tian,Jian Wang,Yi Xiao,Xiaojun Xu,Jinwei Zhang,Peinan Zhao,Tomasz Zok,Eric Westhof +40 more
TL;DR: This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction, where seven groups predicted a lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, using state-of-the-art methods.
Journal ArticleDOI
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme
Zhichao Miao,Ryszard W. Adamiak,Ryszard W. Adamiak,Maciej Antczak,Robert T. Batey,Alexander J. Becka,Marcin Biesiada,Michal J. Boniecki,Janusz M. Bujnicki,Janusz M. Bujnicki,Shi-Jie Chen,Clarence Yu Cheng,Fang-Chieh Chou,Adrian R. Ferré-D'Amaré,Rhiju Das,Wayne K. Dawson,Feng Ding,Nikolay V. Dokholyan,Stanislaw Dunin-Horkawicz,Caleb Geniesse,Kalli Kappel,Wipapat Kladwang,Andrey Krokhotin,Grzegorz Łach,François Major,Thomas H. Mann,Marcin Magnus,Marcin Magnus,Katarzyna Pachulska-Wieczorek,Dinshaw J. Patel,Joseph A. Piccirilli,Mariusz Popenda,Katarzyna J. Purzycka,Aiming Ren,Aiming Ren,Greggory M. Rice,John SantaLucia,Joanna Sarzynska,Marta Szachniuk,Marta Szachniuk,Arpit Tandon,Jeremiah J. Trausch,Siqi Tian,Jian Wang,Kevin M. Weeks,Benfeard Williams,Yi Xiao,Xiaojun Xu,Dong Zhang,Tomasz Zok,Eric Westhof +50 more
TL;DR: A third round of RNA-Puzzles is reported, with a notable need for an algorithm of improvement in the prediction of non-Watson-Crick interactions and the observed high atomic clash scores.
Journal ArticleDOI
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
Zhichao Miao,Zhichao Miao,Ryszard W. Adamiak,Ryszard W. Adamiak,Maciej Antczak,Maciej Antczak,Michal J. Boniecki,Janusz M. Bujnicki,Shi-Jie Chen,Clarence Yu Cheng,Yi Cheng,Fang-Chieh Chou,Rhiju Das,Nikolay V. Dokholyan,Feng Ding,Caleb Geniesse,Yangwei Jiang,Astha Joshi,Andrey Krokhotin,Andrey Krokhotin,Marcin Magnus,Olivier Mailhot,François Major,Thomas H. Mann,Paweł Piątkowski,Radoslaw Pluta,Mariusz Popenda,Joanna Sarzynska,Li-Zhen Sun,Marta Szachniuk,Marta Szachniuk,Siqi Tian,Jian Wang,Jun Wang,Andrew M. Watkins,Jakub Wiedemann,Jakub Wiedemann,Yi Xiao,Xiaojun Xu,Joseph D. Yesselman,Dong Zhang,Yi Zhang,Zhenzhen Zhang,Chenhan Zhao,Peinan Zhao,Yuanzhe Zhou,Tomasz Zok,Adriana Żyła,Aiming Ren,Robert T. Batey,Barbara L. Golden,Lin Huang,Lin Huang,David M.J. Lilley,Yijin Liu,Dinshaw J. Patel,Eric Westhof +56 more
TL;DR: It is illustrated that correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligandbinding modes can be only predicted with low resolution and accurate ligand binding prediction still remains out of reach.
Journal ArticleDOI
iFoldRNA v2: folding RNA with constraints
TL;DR: A new version of the iFoldRNA server is presented that permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides, and a significant benefit provided by integration of experimental data and computational methods is demonstrated.
Journal ArticleDOI
Computational design of chemogenetic and optogenetic split proteins
Onur Dagliyan,Andrey Krokhotin,Andrey Krokhotin,Irem Ozkan-Dagliyan,Alexander Deiters,Channing J. Der,Klaus M. Hahn,Nikolay V. Dokholyan,Nikolay V. Dokholyan +8 more
TL;DR: An automated approach to design effective split proteins regulated by a ligand or by light (SPELL) which uses a split energy scoring function to identify optimal protein split sites and reduces spontaneous assembly.