Publications by authors named "Ivan Anishchenko"

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Computed structures of core eukaryotic protein complexes.
Ian R Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov, Jing Zhang, Travis J Ness, Sudeep Banjade, Saket R Bagde

Science· December 2021

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Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer

Science· August 2021

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Modeling protein-small molecule conformational ensembles with PLACER.
Ivan Anishchenko, Yakov Kipnis, Indrek Kalvet, Guangfeng Zhou, Rohith Krishna

Proc Natl Acad Sci U S A· November 2025

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Modeling protein-small molecule conformational ensembles with PLACER.
Ivan Anishchenko, Yakov Kipnis, Indrek Kalvet, Guangfeng Zhou, Rohith Krishna

bioRxiv· September 2025

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Computational design of serine hydrolases.
Anna Lauko, Samuel J Pellock, Kiera H Sumida, Ivan Anishchenko, David Juergens

Science· April 2025

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Atomic context-conditioned protein sequence design using LigandMPNN.
Justas Dauparas, Gyu Rie Lee, Robert Pecoraro, Linna An, Ivan Anishchenko

Nat Methods· April 2025

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Protein interactions in human pathogens revealed through deep learning.
Ian R Humphreys, Jing Zhang, Minkyung Baek, Yaxi Wang, Aditya Krishnakumar, Ivan Anishchenko

Nat Microbiol· October 2024

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Binding and sensing diverse small molecules using shape-complementary pseudocycles.
Linna An, Meerit Said, Long Tran, Sagardip Majumder, Inna Goreshnik, Ivan Anishchenko

Science· July 2024

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Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Ivan Anishchenko

Science· April 2024

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Essential and virulence-related protein interactions of pathogens revealed through deep learning.
Ian R Humphreys, Jing Zhang, Minkyung Baek, Yaxi Wang, Aditya Krishnakumar, Ivan Anishchenko

bioRxiv· April 2024

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Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.
Minkyung Baek, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, David Baker

Nat Methods· January 2024

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De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.
Linna An, Meerit Said, Long Tran, Sagardip Majumder, Inna Goreshnik, Ivan Anishchenko

bioRxiv· December 2023

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De novo design of luciferases using deep learning.
Andy Hsien-Wei Yeh, Christoffer Norn, Yakov Kipnis, Doug Tischer, Samuel J Pellock, Ivan Anishchenko

Nature· February 2023

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Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar

Brief Bioinform· July 2022

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Scaffolding protein functional sites using deep learning.
Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Joseph L Watson, Ivan Anishchenko

Science· July 2022

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Protein oligomer modeling guided by predicted interchain contacts in CASP14.
Minkyung Baek, Ivan Anishchenko, Hahnbeom Park, Ian R Humphreys, David Baker

Proteins· December 2021

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Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14.
Ivan Anishchenko, Minkyung Baek, Hahnbeom Park, Naozumi Hiranuma, David E Kim

Proteins· December 2021

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The trRosetta server for fast and accurate protein structure prediction.
Zongyang Du, Hong Su, Wenkai Wang, Lisha Ye, Hong Wei, Ivan Anishchenko

Nat Protoc· December 2021

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De novo protein design by deep network hallucination.
Ivan Anishchenko, Samuel J Pellock, Tamuka M Chidyausiku, Theresa A Ramelot, Sergey Ovchinnikov

Nature· December 2021

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Protein sequence design by conformational landscape optimization.
Christoffer Norn, Basile I M Wicky, David Juergens, Sirui Liu, David Kim, Ivan Anishchenko

Proc Natl Acad Sci U S A· March 2021

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In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19.
Isabelle Q Phan, Sandhya Subramanian, David Kim, Michael Murphy, Deleah Pettie, Ivan Anishchenko

Sci Rep· February 2021

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Improved protein structure refinement guided by deep learning based accuracy estimation.
Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas

Nat Commun· February 2021

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Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.
Daniel P Farrell, Ivan Anishchenko, Shabih Shakeel, Anna Lauko, Lori A Passmore

IUCrJ· September 2020

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Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Hersh K Bhargava, Keisuke Tabata, Jordan M Byck, Maho Hamasaki, Daniel P Farrell, Ivan Anishchenko

Proc Natl Acad Sci U S A· July 2020

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

Proc Natl Acad Sci U S A· January 2020

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