Petras Kundrotas
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A structural biology community assessment of AlphaFold2 applications M Akdel, DEV Pires, EP Pardo, J Jänes, AO Zalevsky, B Mészáros, … Nature Structural & Molecular Biology 29 (11), 1056-1067, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:eflP2zaiRacC
Templates are available to model nearly all complexes of structurally characterized proteins PJ Kundrotas, Z Zhu, J Janin, IA Vakser Proceedings of the National Academy of Sciences 109 (24), 9438-9441, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:u5HHmVD_uO8C
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, … Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:RYcK_YlVTxYC
Towards a structurally resolved human protein interaction network DF Burke, P Bryant, I Barrio-Hernandez, D Memon, G Pozzati, A Shenoy, … Nature Structural & Molecular Biology 30 (2), 216-225, 2023 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:q3oQSFYPqjQC
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search P Bryant, G Pozzati, W Zhu, A Shenoy, P Kundrotas, A Elofsson Nature communications 13 (1), 6028, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:HE397vMXCloC
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, … Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:WbkHhVStYXYC
Electrostatic properties of protein-protein complexes PJ Kundrotas, E Alexov Biophysical journal 91 (5), 1724-1736, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:u-x6o8ySG0sC
Docking by structural similarity at protein‐protein interfaces R Sinha, PJ Kundrotas, IA Vakser Proteins: Structure, Function, and Bioinformatics 78 (15), 3235-3241, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:qjMakFHDy7sC
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, … Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:VOx2b1Wkg3QC
Dockground: a comprehensive data resource for modeling of protein complexes PJ Kundrotas, I Anishchenko, T Dauzhenka, I Kotthoff, D Mnevets, … Protein Science 27 (1), 172-181, 2018 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:4OULZ7Gr8RgC
Optimization of electrostatic interactions in protein-protein complexes K Brock, K Talley, K Coley, P Kundrotas, E Alexov Biophysical journal 93 (10), 3340-3352, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:IjCSPb-OGe4C
PROTCOM: searchable database of protein complexes enhanced with domain–domain structures PJ Kundrotas, E Alexov Nucleic acids research 35 (suppl1), D575-D579, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationfor_view=JvYJSc4AAAAJ:d1gkVwhDpl0C
Predicting 3D structures of protein-protein complexes IA Vakser, P Kundrotas Current pharmaceutical biotechnology 9 (2), 57-66, 2008 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:2osOgNQ5qMEC
Blind prediction of interfacial water positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, … Proteins: Structure, Function, and Bioinformatics 82 (4), 620-632, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:Se3iqnhoufwC
On the electrostatic component of protein-protein binding free energy K Talley, C Ng, M Shoppell, P Kundrotas, E Alexov PMC biophysics 1, 1-23, 2008 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:W7OEmFMy1HYC
Homology-based modeling of 3D structures of protein–protein complexes using alignments of modified sequence profiles PJ Kundrotas, MF Lensink, E Alexov International journal of biological macromolecules 43 (2), 198-208, 2008 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:UeHWp8X0CEIC
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives PJ Kundrotas, EG Alexov BMC bioinformatics 7, 1-9, 2006 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:9yKSN-GCB0IC
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes W Zhu, A Shenoy, P Kundrotas, A Elofsson Bioinformatics 39 (7), btad424, 2023 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:AXPGKjj_ei8C
GWIDD: genome-wide protein docking database PJ Kundrotas, Z Zhu, IA Vakser Nucleic acids research 38 (suppl1), D513-D517, 2010 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:Y0pCki6qDkC
On the Ising model for the simple cubic lattice R Häggkvist, A Rosengren, PH Lundow, K Markström, D Andrén, … Advances in Physics 56 (5), 653-755, 2007 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=JvYJSc4AAAAJ&citationforview=JvYJSc4AAAAJ:ufrVoPGSRksC
Youtube Title: Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
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Youtube Channel Name: Morris Chukhman
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
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Youtube Title: #67 AlphaFold and variant effect prediction with Amelie Stein
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Youtube Channel Name: the bioinformatics chat
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#67 AlphaFold and variant effect prediction with Amelie Stein
Youtube Title: #65 AlphaFold and protein interactions with Pedro Beltrao
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Youtube Channel Name: the bioinformatics chat
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#65 AlphaFold and protein interactions with Pedro Beltrao
Youtube Title: High Throughput Structural Bioinformatics
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Youtube Channel Name: ELIXIR Europe
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High Throughput Structural Bioinformatics
Youtube Title: #66 AlphaFold and shape-mers with Janani Durairaj
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Youtube Channel Name: the bioinformatics chat
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#66 AlphaFold and shape-mers with Janani Durairaj
Youtube Title: hu.MAP 2.0: integration of over 15,000 proteomic… - Kevin Drew - NetBio - Abstract - ISMB 2022
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Youtube Channel Name: ISCB
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hu.MAP 2.0: integration of over 15,000 proteomic... - Kevin Drew - NetBio - Abstract - ISMB 2022
Youtube Title: Lecture by Christopher Thornton (National Geographic Society)
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Youtube Channel Name: Brown University
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Lecture by Christopher Thornton (National Geographic Society)
Youtube Title: Expert Discussion “Development of Science and Technology in the Arctic”
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Youtube Channel Name: THE NORTHERN FORUM
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Expert Discussion “Development of Science and Technology in the Arctic”
Youtube Title: Ten Walls feat. Daddy Was A Milkman - INK (Extended)
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Ten Walls feat. Daddy Was A Milkman - INK (Extended)
Youtube Title: Towards a Complete Structural Map of the Human Proteome… - Arne Elofson - 3D-SIG - ISMB/ECCB 2023
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Youtube Channel Name: ISCB
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Towards a Complete Structural Map of the Human Proteome... - Arne Elofson - 3D-SIG - ISMB/ECCB 2023
Youtube Title: Kastytis Kundrotas 1986 - 2014
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Youtube Channel Name: Monika Remeikytė
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Kastytis Kundrotas 1986 - 2014
Youtube Title: Introduction 2017 live recording
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Youtube Channel Name: Introduction to Bioinformatics by Arne Elofsson at Stockholm University
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Introduction 2017 live recording
Youtube Title: Amazon Deforestation from American Soy and Wheat Conglomerates
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Youtube Channel Name: Matthew at My Health Forward
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Amazon Deforestation from American Soy and Wheat Conglomerates
Youtube Title: Arkadijus Vinokuras
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Youtube Channel Name: Arkadijus Vinokur
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Arkadijus Vinokuras
Youtube Title: Žurnalisto, poeto ir prozininko P.Žemkausko 2013 m. išleistų knygų sutiktuvės
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Youtube Channel Name: kaunomenas
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Žurnalisto, poeto ir prozininko P.Žemkausko 2013 m. išleistų knygų sutiktuvės
Youtube Title: Katė
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Youtube Channel Name: Gastauta
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Katė