Results 21 to 30 of about 2,570,021 (252)
Binding Affinity via Docking: Fact and Fiction
Molecules, 2018 In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known ...
Tatu Pantsar, Antti Poso
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A Beginner’s Guide to Molecular Docking
Sciences of Phytochemistry, 2022 In this opinion, the basics of molecular docking (MD) such as binding affinity, binding pose, and ligand interactions with common docking-related terminologies (Apo protein, positive control, native ligand, co-crystal inhibitors) are discussed.
James H. Zothantluanga, Dipak Chetia
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GRAM: A True Null Model for Relative Binding Affinity Predictions [PDF]
, 2019 Relative binding affinity prediction is a critical component in computer aided drug design. Significant amount of effort has been dedicated to developing rapid and reliable in silico methods.
Alan P., Graves +2 more
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PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Journal of Cheminformatics, 2023 Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug’s efficacy and side effects.
Ammar Ammar +3 more
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Indonesian Journal of Chemistry, 2022 Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity.
Umi Baroroh +4 more
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AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using the Ensemble of 3D-Convolutional Neural Network [PDF]
, 2020 Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient and successful rational drug design. In this work, a new neural network model that predicts the binding affinity of a protein-ligand complex structure is ...
Yongbeom, Kwon +3 more
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Inhibition of sequestration of human B-2 bradykinin receptor by phenylarsine oxide or sucrose allows determination of a receptor affinity shift and ligand dissociation in intact cells [PDF]
, 2004 Depending on their interaction with intracellular proteins, G proteincoupled receptors (GPCR) often display different affinities for agonists at 37degreesC. Determining the affinity at that temperature is often difficult in intact cells as most GPCRs are
Faussner, Alexander +3 more
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Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning [PDF]
, 2023 Rational structure-based drug design relies on accurate predictions of protein-ligand binding affinity from structural molecular information. Some of the existing deep learning approaches for this purpose have been criticized for insufficiently capturing
Sereina, Riniker +3 more
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New Journal of Physics, 2021 The specificity of molecular recognition is important for molecular self-organization. A prominent example is the biological cell where a myriad of different molecular receptor pairs recognize their binding partners with astonishing accuracy within a ...
Marc Schenkelberger +5 more
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PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees
Frontiers in Genetics, 2019 Protein-RNA interactions play essential roles in many biological aspects. Quantifying the binding affinity of protein-RNA complexes is helpful to the understanding of protein-RNA recognition mechanisms and identification of strong binding partners.
Lei Deng, Lei Deng, Wenyi Yang, Hui Liu
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