I Anishchenko

Affiliations

Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.

ORCID: 0000-0003-3645-2044

Publications (29)

Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking.

Proteins

Avec: Kathryn A Porter , Dzmitry Padhorny , Israel Desta , Mikhail Ignatov , Dmitri Beglov , Sergei Kotelnikov , Zhuyezi Sun , Andrey Alekseenko , Ivan Anishchenko , Qian Cong , Sergey Ovchinnikov , David Baker , Sandor Vajda , Dima Kozakov

Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.)

Avec: Minkyung Baek , Frank DiMaio , Ivan Anishchenko , Justas Dauparas , Sergey Ovchinnikov , Gyu Rie Lee , Jue Wang , Qian Cong , Lisa N Kinch , R Dustin Schaeffer , Claudia Millán , Hahnbeom Park , Carson Adams , Caleb R Glassman , Andy DeGiovanni , Jose H Pereira , Andria V Rodrigues , Alberdina A van Dijk , Ana C Ebrecht , Diederik J Opperman , Theo Sagmeister , Christoph Buhlheller , Tea Pavkov-Keller , Manoj K Rathinaswamy , Udit Dalwadi , Calvin K Yip , John E Burke , K Christopher Garcia , Nick V Grishin , Paul D Adams , Randy J Read , David Baker

De novo design of luciferases using deep learning.

Nature

Avec: Andy Hsien-Wei Yeh , Christoffer Norn , Yakov Kipnis , Doug Tischer , Samuel J Pellock , Declan Evans , Pengchen Ma , Gyu Rie Lee , Jason Z Zhang , Ivan Anishchenko , Brian Coventry , Longxing Cao , Justas Dauparas , Samer Halabiya , Michelle DeWitt , Lauren Carter , K N Houk , David Baker

Protein interaction networks revealed by proteome coevolution.

Science (New York, N.Y.)

Avec: Qian Cong , Ivan Anishchenko , Sergey Ovchinnikov , David Baker

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.

Briefings in bioinformatics

Avec: Neeladri Sen , Ivan Anishchenko , Nicola Bordin , Ian Sillitoe , Sameer Velankar , David Baker , Christine Orengo

Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.

Nature methods

Avec: Minkyung Baek , Ryan McHugh , Ivan Anishchenko , Hanlun Jiang , David Baker , Frank DiMaio

Scaffolding protein functional sites using deep learning.

Science (New York, N.Y.)

Avec: Jue Wang , Sidney Lisanza , David Juergens , Doug Tischer , Joseph L Watson , Karla M Castro , Robert Ragotte , Amijai Saragovi , Lukas F Milles , Minkyung Baek , Ivan Anishchenko , Wei Yang , Derrick R Hicks , Marc Expòsit , Thomas Schlichthaerle , Jung-Ho Chun , Justas Dauparas , Nathaniel Bennett , Basile I M Wicky , Andrew Muenks , Frank DiMaio , Bruno Correia , Sergey Ovchinnikov , David Baker

Robust deep learning-based protein sequence design using ProteinMPNN.

Science (New York, N.Y.)

Avec: J Dauparas , I Anishchenko , N Bennett , H Bai , R J Ragotte , L F Milles , B I M Wicky , A Courbet , R J de Haas , N Bethel , P J Y Leung , T F Huddy , S Pellock , D Tischer , F Chan , B Koepnick , H Nguyen , A Kang , B Sankaran , A K Bera , N P King , D Baker

Does vitamin D affect strength and speed characteristics and testosterone concentration in elite young track and field athletes in the North European summer?

Nutrition journal

Avec: Eduard Bezuglov , Maria Shoshorina , Artemii Lazarev , Anton Emanov , Egana Koroleva , Ilsyuyar Anishchenko , Zbigniew Waśkiewicz , Mikhail Butovskiy , Ryland Morgans

Essential and virulence-related protein interactions of pathogens revealed through deep learning.

bioRxiv : the preprint server for biology

Avec: Ian R Humphreys , Jing Zhang , Minkyung Baek , Yaxi Wang , Aditya Krishnakumar , Jimin Pei , Ivan Anishchenko , Catherine A Tower , Blake A Jackson , Thulasi Warrier , Deborah T Hung , S Brook Peterson , Joseph D Mougous , Qian Cong , David Baker

Protein interactions in human pathogens revealed through deep learning.

Nature microbiology

Modeling protein-small molecule conformational ensembles with ChemNet.

bioRxiv : the preprint server for biology

Avec: Ivan Anishchenko , Yakov Kipnis , Indrek Kalvet , Guangfeng Zhou , Rohith Krishna , Samuel J Pellock , Anna Lauko , Gyu Rie Lee , Linna An , Justas Dauparas , Frank DiMaio , David Baker

High-accuracy refinement using Rosetta in CASP13.

Proteins

Avec: Hahnbeom Park , Gyu Rie Lee , David E Kim , Ivan Anishchenko , Qian Cong , David Baker

Protein contact prediction using metagenome sequence data and residual neural networks.

Bioinformatics (Oxford, England)

Avec: Qi Wu , Zhenling Peng , Ivan Anishchenko , Qian Cong , David Baker , Jianyi Yang

Protein oligomer modeling guided by predicted interchain contacts in CASP14.

Proteins

Avec: Minkyung Baek , Ivan Anishchenko , Hahnbeom Park , Ian R Humphreys , David Baker

Improved protein structure refinement guided by deep learning based accuracy estimation.

Nature communications

Avec: Naozumi Hiranuma , Hahnbeom Park , Minkyung Baek , Ivan Anishchenko , Justas Dauparas , David Baker

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19.

Scientific reports

Avec: Isabelle Q Phan , Sandhya Subramanian , David Kim , Michael Murphy , Deleah Pettie , Lauren Carter , Ivan Anishchenko , Lynn K Barrett , Justin Craig , Logan Tillery , Roger Shek , Whitney E Harrington , David M Koelle , Anna Wald , David Veesler , Neil King , Jim Boonyaratanakornkit , Nina Isoherranen , Alexander L Greninger , Keith R Jerome , Helen Chu , Bart Staker , Lance Stewart , Peter J Myler , Wesley C Van Voorhis

De novo protein design by deep network hallucination.

Nature

Avec: Ivan Anishchenko , Samuel J Pellock , Tamuka M Chidyausiku , Theresa A Ramelot , Sergey Ovchinnikov , Jingzhou Hao , Khushboo Bafna , Christoffer Norn , Alex Kang , Asim K Bera , Frank DiMaio , Lauren Carter , Cameron M Chow , Gaetano T Montelione , David Baker

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Science (New York, N.Y.)

Avec: Rohith Krishna , Jue Wang , Woody Ahern , Pascal Sturmfels , Preetham Venkatesh , Indrek Kalvet , Gyu Rie Lee , Felix S Morey-Burrows , Ivan Anishchenko , Ian R Humphreys , Ryan McHugh , Dionne Vafeados , Xinting Li , George A Sutherland , Andrew Hitchcock , C Neil Hunter , Alex Kang , Evans Brackenbrough , Asim K Bera , Minkyung Baek , Frank DiMaio , David Baker

Gene ontology improves template selection in comparative protein docking.

Proteins

Avec: Anna Hadarovich , Ivan Anishchenko , Alexander V Tuzikov , Petras J Kundrotas , Ilya A Vakser

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Hersh K Bhargava , Keisuke Tabata , Jordan M Byck , Maho Hamasaki , Daniel P Farrell , Ivan Anishchenko , Frank DiMaio , Young Jun Im , Tamotsu Yoshimori , James H Hurley

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.

IUCrJ

Avec: Daniel P Farrell , Ivan Anishchenko , Shabih Shakeel , Anna Lauko , Lori A Passmore , David Baker , Frank DiMaio

Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14.

Proteins

Avec: Ivan Anishchenko , Minkyung Baek , Hahnbeom Park , Naozumi Hiranuma , David E Kim , Justas Dauparas , Sanaa Mansoor , Ian R Humphreys , David Baker

Protein sequence design by conformational landscape optimization.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Christoffer Norn , Basile I M Wicky , David Juergens , Sirui Liu , David Kim , Doug Tischer , Brian Koepnick , Ivan Anishchenko , Auteur inconnu , David Baker , Sergey Ovchinnikov

Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.)

Avec: Ian R Humphreys , Jimin Pei , Minkyung Baek , Aditya Krishnakumar , Ivan Anishchenko , Sergey Ovchinnikov , Jing Zhang , Travis J Ness , Sudeep Banjade , Saket R Bagde , Viktoriya G Stancheva , Xiao-Han Li , Kaixian Liu , Zhi Zheng , Daniel J Barrero , Upasana Roy , Jochen Kuper , Israel S Fernández , Barnabas Szakal , Dana Branzei , Josep Rizo , Caroline Kisker , Eric C Greene , Sue Biggins , Scott Keeney , Elizabeth A Miller , J Christopher Fromme , Tamara L Hendrickson , Qian Cong , David Baker

Binding and sensing diverse small molecules using shape-complementary pseudocycles.

Science (New York, N.Y.)

Avec: Linna An , Meerit Said , Long Tran , Sagardip Majumder , Inna Goreshnik , Gyu Rie Lee , David Juergens , Justas Dauparas , Ivan Anishchenko , Brian Coventry , Asim K Bera , Alex Kang , Paul M Levine , Valentina Alvarez , Arvind Pillai , Christoffer Norn , David Feldman , Dmitri Zorine , Derrick R Hicks , Xinting Li , Mariana Garcia Sanchez , Dionne K Vafeados , Patrick J Salveson , Anastassia A Vorobieva , David Baker

Improved protein structure prediction using predicted interresidue orientations.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Jianyi Yang , Ivan Anishchenko , Hahnbeom Park , Zhenling Peng , Sergey Ovchinnikov , David Baker

The trRosetta server for fast and accurate protein structure prediction.

Nature protocols

Avec: Zongyang Du , Hong Su , Wenkai Wang , Lisha Ye , Hong Wei , Zhenling Peng , Ivan Anishchenko , David Baker , Jianyi Yang

De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.

bioRxiv : the preprint server for biology

Réseau de co-auteurs

Ivan Anishchenko 27 collaborations

David Baker 24 collaborations

Minkyung Baek 10 collaborations

Qian Cong 8 collaborations

Sergey Ovchinnikov 8 collaborations

Frank DiMaio 8 collaborations

Justas Dauparas 8 collaborations

Gyu Rie Lee 7 collaborations

Hahnbeom Park 6 collaborations

Ian R Humphreys 6 collaborations

Christoffer Norn 5 collaborations

David Juergens 4 collaborations

Alex Kang 4 collaborations

Asim K Bera 4 collaborations

Jue Wang 3 collaborations

Doug Tischer 3 collaborations

Samuel J Pellock 3 collaborations

Brian Coventry 3 collaborations

Lauren Carter 3 collaborations

Derrick R Hicks 3 collaborations

Jing Zhang 3 collaborations

Aditya Krishnakumar 3 collaborations

Jimin Pei 3 collaborations

Linna An 3 collaborations

Zhenling Peng 3 collaborations

Jianyi Yang 3 collaborations

Xinting Li 3 collaborations

Yakov Kipnis 2 collaborations

Ryan McHugh 2 collaborations

Basile I M Wicky 2 collaborations

Yaxi Wang 2 collaborations

Catherine A Tower 2 collaborations

Blake A Jackson 2 collaborations

Thulasi Warrier 2 collaborations

Deborah T Hung 2 collaborations

S Brook Peterson 2 collaborations

Joseph D Mougous 2 collaborations

Indrek Kalvet 2 collaborations

Rohith Krishna 2 collaborations

Anna Lauko 2 collaborations

David E Kim 2 collaborations

Naozumi Hiranuma 2 collaborations

David Kim 2 collaborations

Daniel P Farrell 2 collaborations

Meerit Said 2 collaborations

Long Tran 2 collaborations

Sagardip Majumder 2 collaborations

Inna Goreshnik 2 collaborations

Paul M Levine 2 collaborations

Valentina Alvarez 2 collaborations

Arvind Pillai 2 collaborations

David Feldman 2 collaborations

Dmitri Zorine 2 collaborations

Mariana Garcia Sanchez 2 collaborations

Dionne K Vafeados 2 collaborations

Patrick J Salveson 2 collaborations

Anastassia A Vorobieva 2 collaborations

Kathryn A Porter 1 collaboration

Dzmitry Padhorny 1 collaboration

Israel Desta 1 collaboration

Mikhail Ignatov 1 collaboration

Dmitri Beglov 1 collaboration

Sergei Kotelnikov 1 collaboration

Zhuyezi Sun 1 collaboration

Andrey Alekseenko 1 collaboration

Sandor Vajda 1 collaboration

Dima Kozakov 1 collaboration

Lisa N Kinch 1 collaboration

R Dustin Schaeffer 1 collaboration

Claudia Millán 1 collaboration

Carson Adams 1 collaboration

Caleb R Glassman 1 collaboration

Andy DeGiovanni 1 collaboration

Jose H Pereira 1 collaboration

Andria V Rodrigues 1 collaboration

Alberdina A van Dijk 1 collaboration

Ana C Ebrecht 1 collaboration

Diederik J Opperman 1 collaboration

Theo Sagmeister 1 collaboration

Christoph Buhlheller 1 collaboration

Tea Pavkov-Keller 1 collaboration

Manoj K Rathinaswamy 1 collaboration

Udit Dalwadi 1 collaboration

Calvin K Yip 1 collaboration

John E Burke 1 collaboration

K Christopher Garcia 1 collaboration

Nick V Grishin 1 collaboration

Paul D Adams 1 collaboration

Randy J Read 1 collaboration

Andy Hsien-Wei Yeh 1 collaboration

Declan Evans 1 collaboration

Pengchen Ma 1 collaboration

Jason Z Zhang 1 collaboration

Longxing Cao 1 collaboration

Samer Halabiya 1 collaboration

Michelle DeWitt 1 collaboration

K N Houk 1 collaboration

Neeladri Sen 1 collaboration

Nicola Bordin 1 collaboration

Ian Sillitoe 1 collaboration

Sameer Velankar 1 collaboration

Christine Orengo 1 collaboration

Hanlun Jiang 1 collaboration

Sidney Lisanza 1 collaboration

Joseph L Watson 1 collaboration

Karla M Castro 1 collaboration

Robert Ragotte 1 collaboration

Amijai Saragovi 1 collaboration

Lukas F Milles 1 collaboration

Wei Yang 1 collaboration

Marc Expòsit 1 collaboration

Thomas Schlichthaerle 1 collaboration

Jung-Ho Chun 1 collaboration

Nathaniel Bennett 1 collaboration

Andrew Muenks 1 collaboration

Bruno Correia 1 collaboration

J Dauparas 1 collaboration

N Bennett 1 collaboration

H Bai 1 collaboration

R J Ragotte 1 collaboration

L F Milles 1 collaboration

B I M Wicky 1 collaboration

A Courbet 1 collaboration

R J de Haas 1 collaboration

N Bethel 1 collaboration

P J Y Leung 1 collaboration

T F Huddy 1 collaboration

S Pellock 1 collaboration

D Tischer 1 collaboration

F Chan 1 collaboration

B Koepnick 1 collaboration

H Nguyen 1 collaboration

A Kang 1 collaboration

B Sankaran 1 collaboration

A K Bera 1 collaboration

N P King 1 collaboration

D Baker 1 collaboration

Eduard Bezuglov 1 collaboration

Maria Shoshorina 1 collaboration

Artemii Lazarev 1 collaboration

Anton Emanov 1 collaboration

Egana Koroleva 1 collaboration

Ilsyuyar Anishchenko 1 collaboration

Zbigniew Waśkiewicz 1 collaboration

Mikhail Butovskiy 1 collaboration

Ryland Morgans 1 collaboration

Guangfeng Zhou 1 collaboration

Qi Wu 1 collaboration

Isabelle Q Phan 1 collaboration

Sandhya Subramanian 1 collaboration

Michael Murphy 1 collaboration

Deleah Pettie 1 collaboration

Lynn K Barrett 1 collaboration

Justin Craig 1 collaboration

Logan Tillery 1 collaboration

Roger Shek 1 collaboration

Whitney E Harrington 1 collaboration

David M Koelle 1 collaboration

Anna Wald 1 collaboration

David Veesler 1 collaboration

Neil King 1 collaboration

Jim Boonyaratanakornkit 1 collaboration

Nina Isoherranen 1 collaboration

Alexander L Greninger 1 collaboration

Keith R Jerome 1 collaboration

Helen Chu 1 collaboration

Bart Staker 1 collaboration

Lance Stewart 1 collaboration

Peter J Myler 1 collaboration

Wesley C Van Voorhis 1 collaboration

Tamuka M Chidyausiku 1 collaboration

Theresa A Ramelot 1 collaboration

Jingzhou Hao 1 collaboration

Khushboo Bafna 1 collaboration

Cameron M Chow 1 collaboration

Gaetano T Montelione 1 collaboration

Woody Ahern 1 collaboration

Pascal Sturmfels 1 collaboration

Preetham Venkatesh 1 collaboration

Felix S Morey-Burrows 1 collaboration

Dionne Vafeados 1 collaboration

George A Sutherland 1 collaboration

Andrew Hitchcock 1 collaboration

C Neil Hunter 1 collaboration

Evans Brackenbrough 1 collaboration

Anna Hadarovich 1 collaboration

Alexander V Tuzikov 1 collaboration

Petras J Kundrotas 1 collaboration

Ilya A Vakser 1 collaboration

Hersh K Bhargava 1 collaboration

Keisuke Tabata 1 collaboration

Jordan M Byck 1 collaboration

Maho Hamasaki 1 collaboration

Young Jun Im 1 collaboration

Tamotsu Yoshimori 1 collaboration

James H Hurley 1 collaboration

Shabih Shakeel 1 collaboration

Lori A Passmore 1 collaboration

Sanaa Mansoor 1 collaboration

Sirui Liu 1 collaboration

Brian Koepnick 1 collaboration

None None 1 collaboration

Travis J Ness 1 collaboration

Sudeep Banjade 1 collaboration

Saket R Bagde 1 collaboration

Viktoriya G Stancheva 1 collaboration

Xiao-Han Li 1 collaboration

Kaixian Liu 1 collaboration

Zhi Zheng 1 collaboration

Daniel J Barrero 1 collaboration

Upasana Roy 1 collaboration

Jochen Kuper 1 collaboration

Israel S Fernández 1 collaboration

Barnabas Szakal 1 collaboration

Dana Branzei 1 collaboration

Josep Rizo 1 collaboration

Caroline Kisker 1 collaboration

Eric C Greene 1 collaboration

Sue Biggins 1 collaboration

Scott Keeney 1 collaboration

Elizabeth A Miller 1 collaboration

J Christopher Fromme 1 collaboration

Tamara L Hendrickson 1 collaboration

Zongyang Du 1 collaboration

Hong Su 1 collaboration

Wenkai Wang 1 collaboration

Lisha Ye 1 collaboration

Hong Wei 1 collaboration