AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein–Ligand Association
Sign Up to like & getrecommendations! Published in 2018 at "ChemMedChem"
DOI: 10.1002/cmdc.201700564
Abstract: Unquestionably, water appears to be an active player in the noncovalent protein–ligand binding process, as it can either bridge interactions between protein and ligand or can be replaced by the bound ligand. Accordingly, in the… read more here.
Keywords: water; hydration sites; water molecules; association ... See more keywords
Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.
Sign Up to like & getrecommendations! Published in 2018 at "International journal for numerical methods in biomedical engineering"
DOI: 10.1002/cnm.2914
Abstract: Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein-ligand binding affinities is… read more here.
Keywords: persistent homology; topology; protein ligand; ligand binding ... See more keywords
PharmRF: A machine‐learning scoring function to identify the best protein‐ligand complexes for structure‐based pharmacophore screening with high enrichments
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26840
Abstract: Structure‐based pharmacophore models are often developed by selecting a single protein‐ligand complex with good resolution and better binding affinity data which prevents the analysis of other structures having a similar potential to act as better… read more here.
Keywords: based pharmacophore; pharmrf; structure based; protein ligand ... See more keywords
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26940
Abstract: Fragment molecular orbital (FMO) method is a powerful computational tool for structure‐based drug design, in which protein–ligand interactions can be described by the inter‐fragment interaction energy (IFIE) and its pair interaction energy decomposition analysis (PIEDA).… read more here.
Keywords: interaction energy; fragment molecular; energy; protein ligand ... See more keywords
Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Informatics"
DOI: 10.1002/minf.202100248
Abstract: Accurate prediction of binding poses is crucial to structure‐based drug design. We employ two powerful artificial intelligence (AI) approaches, data‐mining and machine‐learning, to design artificial neural network (ANN) based pose‐scoring function. It is a simple… read more here.
Keywords: function; scoring function; machine learning; mbi score ... See more keywords
Protein Ligand Nanopattern Size Selects for Cellular Adhesion via Hemidesmosomes over Focal Adhesions
Sign Up to like & getrecommendations! Published in 2022 at "Small Methods"
DOI: 10.1002/smtd.202200152
Abstract: Hemidesmosomes (HDs) are multiprotein complexes that firmly anchor epidermal cells to the basement membrane of skin through the interconnection of the cytoplasmic intermediate filaments with extracellular laminin 332 (Ln332). Considerably less attention has been paid… read more here.
Keywords: adhesion; hds; via hemidesmosomes; size ... See more keywords
Repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein–ligand binding reaction measured by isothermal titration calorimetry
Sign Up to like & getrecommendations! Published in 2018 at "European Biophysics Journal"
DOI: 10.1007/s00249-018-1341-z
Abstract: In rational drug design, it is important to determine accurately and with high precision the binding constant (the affinity or the change in Gibbs energy, ∆G), the change in enthalpy (ΔH), and the entropy change… read more here.
Keywords: accuracy; isothermal titration; titration calorimetry; protein ligand ... See more keywords
LiGRO: a graphical user interface for protein–ligand molecular dynamics
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-017-3475-9
Abstract: To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands… read more here.
Keywords: protein; molecular dynamics; topology; interface ... See more keywords
Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-018-3820-7
Abstract: Ensemble methods are gaining more importance in structure-based approaches as single protein-ligand complexes strongly influence the outcomes of virtual screening. Structure-based pharmacophore modeling based on a single protein-ligand complex with complex feature combinations is often… read more here.
Keywords: ligand complexes; pharmacophore ensemble; ligand; protein ligand ... See more keywords
GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0030-9
Abstract: Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of… read more here.
Keywords: protein; scoring function; galaxydock bp2; score ... See more keywords
Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0046-1
Abstract: A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the… read more here.
Keywords: challenge; poses graph; method; graph matching ... See more keywords