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Journal Abstract Search

154 related items for PubMed ID: 27367467

  • 1. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.
    Sulea T, Vivcharuk V, Corbeil CR, Deprez C, Purisima EO.
    J Chem Inf Model; 2016 Jul 25; 56(7):1292-303. PubMed ID: 27367467
    [Abstract] [Full Text] [Related]

  • 2. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
    Cui Q, Sulea T, Schrag JD, Munger C, Hung MN, Naïm M, Cygler M, Purisima EO.
    J Mol Biol; 2008 Jun 13; 379(4):787-802. PubMed ID: 18479705
    [Abstract] [Full Text] [Related]

  • 3. The solvated interaction energy method for scoring binding affinities.
    Sulea T, Purisima EO.
    Methods Mol Biol; 2012 Jun 13; 819():295-303. PubMed ID: 22183544
    [Abstract] [Full Text] [Related]

  • 4. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise.
    Sulea T, Cui Q, Purisima EO.
    J Chem Inf Model; 2011 Sep 26; 51(9):2066-81. PubMed ID: 21714553
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  • 5. Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen.
    Chen Y, Wiesmann C, Fuh G, Li B, Christinger HW, McKay P, de Vos AM, Lowman HB.
    J Mol Biol; 1999 Nov 05; 293(4):865-81. PubMed ID: 10543973
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  • 6. Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen.
    Li Y, Urrutia M, Smith-Gill SJ, Mariuzza RA.
    Biochemistry; 2003 Jan 14; 42(1):11-22. PubMed ID: 12515535
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  • 7. Antibody Affinity Maturation by Computational Design.
    Kuroda D, Tsumoto K.
    Methods Mol Biol; 2018 Jan 14; 1827():15-34. PubMed ID: 30196490
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  • 8. AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences.
    Jin R, Ye Q, Wang J, Cao Z, Jiang D, Wang T, Kang Y, Xu W, Hsieh CY, Hou T.
    Brief Bioinform; 2024 May 23; 25(4):. PubMed ID: 38960407
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  • 9. Assessment of software methods for estimating protein-protein relative binding affinities.
    Gonzalez TR, Martin KP, Barnes JE, Patel JS, Ytreberg FM.
    PLoS One; 2020 May 23; 15(12):e0240573. PubMed ID: 33347442
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  • 10. AB-Bind: Antibody binding mutational database for computational affinity predictions.
    Sirin S, Apgar JR, Bennett EM, Keating AE.
    Protein Sci; 2016 Feb 23; 25(2):393-409. PubMed ID: 26473627
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  • 11. Machine learning in computational docking.
    Khamis MA, Gomaa W, Ahmed WF.
    Artif Intell Med; 2015 Mar 23; 63(3):135-52. PubMed ID: 25724101
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  • 12. Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations.
    Corrada D, Colombo G.
    J Chem Inf Model; 2013 Nov 25; 53(11):2937-50. PubMed ID: 24168661
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  • 13. Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges.
    Hogues H, Sulea T, Purisima EO.
    J Chem Inf Model; 2016 Jun 27; 56(6):955-64. PubMed ID: 26282162
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  • 14. Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex.
    Kiyoshi M, Caaveiro JM, Miura E, Nagatoishi S, Nakakido M, Soga S, Shirai H, Kawabata S, Tsumoto K.
    PLoS One; 2014 Jun 27; 9(1):e87099. PubMed ID: 24475232
    [Abstract] [Full Text] [Related]

  • 15. Solvated interaction energy: from small-molecule to antibody drug design.
    Purisima EO, Corbeil CR, Gaudreault F, Wei W, Deprez C, Sulea T.
    Front Mol Biosci; 2023 Jun 27; 10():1210576. PubMed ID: 37351549
    [Abstract] [Full Text] [Related]

  • 16. FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data.
    Pearlman DA, Rao BG, Charifson P.
    Proteins; 2008 May 15; 71(3):1519-38. PubMed ID: 18300249
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  • 17. A comparative assessment of ranking accuracies of conventional and machine-learning-based scoring functions for protein-ligand binding affinity prediction.
    Ashtawy HM, Mahapatra NR.
    IEEE/ACM Trans Comput Biol Bioinform; 2012 May 15; 9(5):1301-13. PubMed ID: 22411892
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  • 18. Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform.
    Sulea T, Deprez C, Corbeil CR, Purisima EO.
    Methods Mol Biol; 2023 May 15; 2552():361-374. PubMed ID: 36346603
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  • 19. Engineering protein therapeutics: predictive performances of a structure-based virtual affinity maturation protocol.
    Oberlin M, Kroemer R, Mikol V, Minoux H, Tastan E, Baurin N.
    J Chem Inf Model; 2012 Aug 27; 52(8):2204-14. PubMed ID: 22788756
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  • 20. PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.
    Liu X, Liu J, Zhu T, Zhang L, He X, Zhang JZ.
    J Chem Inf Model; 2016 May 23; 56(5):854-61. PubMed ID: 27088302
    [Abstract] [Full Text] [Related]

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