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MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn
Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end-state MM/GBSA methods to...
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EPDRNA: A Model for Identifying DNA–RNA Binding Sites in Disease-Related Proteins
Protein–DNA and protein–RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are 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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PUResNet: prediction of protein-ligand binding sites using deep residual neural network
BackgroundPredicting protein-ligand binding sites is a fundamental step in understanding the functional characteristics of proteins, which plays a...
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A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors
Janus kinase 2 (JAK2) inhibitors are potential anticancer drugs in the treatment of lymphoma, leukemia, thrombocytosis and particularly...
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Electrochemical carbonyl reduction on single-site M–N–C catalysts
Electrochemical conversion of organic compounds holds promise for advancing sustainable synthesis and catalysis. This study explored electrochemical...
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Enhanced active-site electric field accelerates enzyme catalysis
The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic...
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Identification, characterization and binding sites prediction of calcium transporter-embryo egg-derived egg white peptides
In order to provide an efficient calcium transporter for the development of calcium supplement products, embryo eggs were selected for incubation....
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Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors
Studying the binding processes of G protein-coupled receptors (GPCRs) proteins is of particular interest both to better understand the molecular...
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The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction
Structure-based drug design depends on the detailed knowledge of the three-dimensional (3D) structures of protein–ligand binding complexes, but...
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A Supported Metal Dual-Atom Site Catalyst for Oxygen Reduction: A First-Principles Study
AbstractDual-atom site catalysts with the adjacent metal atomic sites can cooperatively catalyze oxygen reduction reaction (ORR), showing great...
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Deep Learning for Protein–Protein Interaction Site Prediction
Protein–protein interactions (PPIs) are central to cellular functions. Experimental methods for predicting PPIs are well developed but are time and...
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Site-specific encoding of photoactivity and photoreactivity into antibody fragments
Design of biomolecules that perform two or more distinct functions in response to light remains challenging. Here, we have introduced concurrent...
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Exploring the binding mechanism of a small molecular Hsp70-Bim PPI inhibitor through molecular dynamic simulation
ContextThe interface of Hsp70-Bim protein–protein interaction (PPI) has been identified as a specific target for Chronic Myeloid Leukemia (CML)...
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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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Exploring QSAR models for activity-cliff prediction
Introduction and methodologyPairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their...
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In silico Study on Binding Specificities of Cellular Retinol Binding Protein and Its Q108R Mutant
Cellular retinol binding proteins (CRBPs) are industrially important lipocalin proteins which can be potential targets for drug development, scaffold...
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Protein Structure Prediction and Analysis
Why it is important to know this material? Protein structure prediction is one of the hot topics of the modern computational biology. The...
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Web Services for RNA-RNA Interaction Prediction
Non-coding RNAs have various biological functions such as translational regulation, and RNA-RNA interactions play essential roles in the mechanisms...
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Directing CO2 electroreduction pathways for selective C2 product formation using single-site doped copper catalysts
Manipulating the selectivity-determining step in post-C–C coupling is crucial for enhancing C 2 product specificity during electrocatalytic CO 2 ...
