ArticleChemical biology & drug design2012
Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand.
Article in Chemical biology & drug design, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Future Perspective: Harnessing the Power of Artificial Intelligence in the Generation of New Peptide Drugs.Biomolecules · 2024Review
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking.PloS one · 2022Article
- Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.Frontiers in pharmacology · 2022Article
- Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids.PloS one · 2022Article
- Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).Protein science : a publication of the Protein Society · 2018Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
- Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth.The Journal of clinical investigation · 2015Article
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- Human germline antibody gene segments encode polyspecific antibodies.PLoS computational biology · 2013Article
- Small-molecule ligand docking into comparative models with Rosetta.Nature protocols · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Predicting HIV-1 protease/inhibitor binding affinity as the difference between the free energy of the inhibitor bound and unbound state remains difficult as the unbound state exists as an ensemble of conformations with various degrees of flap opening. We improve computational prediction of protease/inhibitor affinity by invoking the hypothesis that the free energy of the unbound state while difficult to predict is less sensitive to mutation. Thereby the HIV-1 protease/inhibitor binding affinity can be approximated with the free energy of the bound state alone. Bound state free energy can be predicted from comparative models of HIV-1 protease mutant/inhibitor complexes. Absolute binding energies are predicted with R = 0.71 and SE = 5.91 kJ/mol. Changes in binding free energy upon mutation can be predicted with R = 0.85 and SE = 4.49 kJ/mol. Resistance mutations that lower inhibitor binding affinity can thereby be recognized early in HIV-1 protease inhibitor development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.