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Bekar-Cesaretli, Ayse A., Khan, Omeir, Nguyen, Thu, Kozakov, Dima, Joseph-Mccarthy, Diane, Vajda, Sandor (2024) Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. Journal of Chemical Information and Modeling, 64 (3) 960-973 doi:10.1021/acs.jcim.3c01761

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Reference TypeJournal (article/letter/editorial)
TitleConservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2
JournalJournal of Chemical Information and Modeling
AuthorsBekar-Cesaretli, Ayse A.Author
Khan, OmeirAuthor
Nguyen, ThuAuthor
Kozakov, DimaAuthor
Joseph-Mccarthy, DianeAuthor
Vajda, SandorAuthor
Year2024 (February 12)Volume64
Issue3
PublisherAmerican Chemical Society (ACS)
DOIdoi:10.1021/acs.jcim.3c01761Search in ResearchGate
Generate Citation Formats
Mindat Ref. ID17156776Long-form Identifiermindat:1:5:17156776:4
GUID0
Full ReferenceBekar-Cesaretli, Ayse A., Khan, Omeir, Nguyen, Thu, Kozakov, Dima, Joseph-Mccarthy, Diane, Vajda, Sandor (2024) Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. Journal of Chemical Information and Modeling, 64 (3) 960-973 doi:10.1021/acs.jcim.3c01761
Plain TextBekar-Cesaretli, Ayse A., Khan, Omeir, Nguyen, Thu, Kozakov, Dima, Joseph-Mccarthy, Diane, Vajda, Sandor (2024) Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. Journal of Chemical Information and Modeling, 64 (3) 960-973 doi:10.1021/acs.jcim.3c01761
In(2024, February) Journal of Chemical Information and Modeling Vol. 64 (3) American Chemical Society (ACS)

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Khan, Omeir, Jones, George, Lazou, Maria, Joseph-McCarthy, Diane, Kozakov, Dima, Beglov, Dmitri, Vajda, Sandor (2024) Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. Journal of Chemical Information and Modeling, 64 (6) 2084-2100 doi:10.1021/acs.jcim.3c01969
Lazou, Maria, Khan, Omeir, Nguyen, Thu, Padhorny, Dzmitry, Kozakov, Dima, Joseph-McCarthy, Diane, Vajda, Sandor (2024) Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much. Proceedings of the National Academy of Sciences, 121 (48). doi:10.1073/pnas.2412719121
Wakefield, Amanda E., Bajusz, Dávid, Kozakov, Dima, Keserű, György M., Vajda, Sandor (2022) Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. Journal of Chemical Information and Modeling, 62 (20) 4937-4954 doi:10.1021/acs.jcim.2c00209
Zerbe, Brandon S., Hall, David R., Vajda, Sandor, Whitty, Adrian, Kozakov, Dima (2012) Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces. Journal of Chemical Information and Modeling, 52 (8) 2236-2244 doi:10.1021/ci300175u
Khan, Omeir; Jones, George; Kozakov, Dima; Beglov, Dmitri; Joseph-McCarthy, Diane; Vajda, Sandor (2025) E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion. Journal of Molecular Biology, 437 (15). doi:10.1016/j.jmb.2025.168956
Wakefield, Amanda E., Yueh, Christine, Beglov, Dmitri, Castilho, Marcelo S., Kozakov, Dima, Keserű, György M., Whitty, Adrian, Vajda, Sandor (2020) Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. Journal of Chemical Information and Modeling, 60 (12) 6612-6623 doi:10.1021/acs.jcim.0c00877
Mottarella, Scott E., Beglov, Dmitri, Beglova, Natalia, Nugent, Matthew A., Kozakov, Dima, Vajda, Sandor (2014) Docking Server for the Identification of Heparin Binding Sites on Proteins. Journal of Chemical Information and Modeling, 54 (7) 2068-2078 doi:10.1021/ci500115j
Moghadasi, Mohammad, Mirzaei, Hanieh, Mamonov, Artem, Vakili, Pirooz, Vajda, Sandor, Paschalidis, Ioannis Ch., Kozakov, Dima (2015) The Impact of Side-Chain Packing on Protein Docking Refinement. Journal of Chemical Information and Modeling, 55 (4) 872-881 doi:10.1021/ci500380a
Hall, David H., Grove, Laurie E., Yueh, Christine, Ngan, Chi Ho, Kozakov, Dima, Vajda, Sandor (2011) Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme. Journal Of The American Chemical Society, 133 (51) 20668-20671 doi:10.1021/ja207914y
Hall, David R., Ngan, Chi Ho, Zerbe, Brandon S., Kozakov, Dima, Vajda, Sandor (2012) Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling, 52 (1) 199-209 doi:10.1021/ci200468p
 
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