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Software for Predicting Binding Free Energy of Protein–Protein Complexes and Their Mutants
Protein–protein binding affinity prediction is important for understanding complex biochemical pathways and to uncover protein interaction networks....
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An overview of the SAMPL8 host–guest binding challenge
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of...
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Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips
Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in...
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Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations
N -geranyl- N ΄-(2-adamantyl)ethane-1,2-diamine (SQ109) is a tuberculosis drug that has high potency against Mycobacterium tuberculosis (Mtb) and may...
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SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations
Host–guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important...
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Cyanine Dye–DNA Interactions: Intercalation, Groove Binding, and Aggregation
The cyanine dyes are among the oldest classes of synthetic compounds but continue to find applications in a variety of fields. In many cases, the...
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Distance plus attention for binding affinity prediction
Protein-ligand binding affinity plays a pivotal role in drug development, particularly in identifying potential ligands for target disease-related...
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A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios
We release a new, high quality data set of 1162 PDE10A inhibitors with experimentally determined binding affinities together with 77 PDE10A X-ray...
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Binding patterns of derivatives of fisetin and chrysin to the enzyme complex cyclin-dependent kinase 6/cyclin D
Clinical inhibitors of cell-cycle regulatory enzyme cyclin-dependent kinase 6 (CDK6) are not free of harmful consequences to human bodies. Flavonoids...
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Automated relative binding free energy calculations from SMILES to ΔΔG
In drug discovery, computational methods are a key part of making informed design decisions and prioritising experiments. In particular, optimizing...
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Structure-based, deep-learning models for protein-ligand binding affinity prediction
The launch of AlphaFold series has brought deep-learning techniques into the molecular structural science. As another crucial problem,...
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Enhanced map** of small-molecule binding sites in cells
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving...
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SARS-CoV-2S-Protein–Ace2 Binding Analysis Using Surface Plasmon Resonance
Surface plasmon resonance (SPR) allows for the label-free determination of the binding affinity and rate constants of bimolecular interactions. Here,...
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A computational approach to optimising laccase-mediated polyethylene oxidation through carbohydrate-binding module fusion
Plastic pollution is a major global concern to the health and wellbeing of all terrestrial and marine life. However, no sustainable method for waste...
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Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics
Peptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on...
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Sialic acid-containing glycolipids mediate binding and viral entry of SARS-CoV-2
Emerging evidence suggests that host glycans influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Here, we reveal that...
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Exploring the binding interactions of NOP receptor with designed natural phytochemical-neuropeptide conjugates: an in silico and SPR study
The Nociceptin/orphanin FQ peptide (NOP) receptor is considered a member of the opioid receptor subfamily of G-protein coupled receptors (GPCRs)...
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Recent progress in analytical strategies of arsenic-binding proteomes in living systems
Arsenic (As) is one of the most concerning elements due to its high exposure risks to organisms and ecosystems. The interaction between arsenicals...
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Structural mechanism for specific binding of chemical compounds to amyloid fibrils
Amyloid fibril is an important pharmaceutical target for diagnostic and therapeutic treatment of neurodegenerative diseases. However, rational design...
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TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection
Drug discovery, especially virtual screening and drug repositioning, can be accelerated through deeper understanding and prediction of Drug Target...
