Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with β‐substituted disaccharides
Sign Up to like & getrecommendations! Published in 2017 at "IUBMB Life"
DOI: 10.1002/iub.1593
Abstract: Crystal structures of jacalin in complex with GlcNAc β‐(1,3) Gal‐β‐OMe and Gal β‐(1,3) Gal‐β‐OMe have been determined. The binding of the ligands to jacalin is similar to that of analogous α‐substituted disaccharides. However, the β‐substituted… read more here.
Keywords: strategy modulating; affinity; distortion; jacalin ... See more keywords
Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Cellular Biochemistry"
DOI: 10.1002/jcb.26435
Abstract: Antibiotic resistance to aminoglycoside group of antibiotics mainly occurs by aminoglycoside kinases (AKs). Thus, targeting AKs from different multidrug resistant (MDR) strains could result into inhibition of AK enzymes and ultimately the resistance. Therefore, the… read more here.
Keywords: different aks; mdr strains; aminoglycoside kinases; virtually screened ... See more keywords
Taba: A Tool to Analyze the Binding Affinity
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26048
Abstract: Evaluation of ligand‐binding affinity using the atomic coordinates of a protein‐ligand complex is a challenge from the computational point of view. The availability of crystallographic structures of complexes with binding affinity data opens the possibility… read more here.
Keywords: methodology; taba tool; affinity; tool analyze ... See more keywords
Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26831
Abstract: Drug discovery pipelines typically involve high‐throughput screening of large amounts of compounds in a search of potential drugs candidates. As a chemical space of small organic molecules is huge, a “navigation” over it urges for… read more here.
Keywords: neural network; binding affinity; affinity; graph ... See more keywords
More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4375
Abstract: In statistical mechanics, it is well known that the huge number of degrees of freedom does not complicate the problem as it seems, but actually greatly simplifies the analysis (e.g., to give a Boltzmann distribution).… read more here.
Keywords: simpler decomposition; ligand binding; binding affinity; decomposition ligand ... See more keywords
Nitrogen-Doped Graphene Nanoscroll Foam with High Diffusion Rate and Binding Affinity for Removal of Organic Pollutants.
Sign Up to like & getrecommendations! Published in 2017 at "Small"
DOI: 10.1002/smll.201603779
Abstract: A nitrogen-doped 3D graphene foam assembled with nanoscroll structure is constructed via a facile mild-heating methodology using a polar molecule of formamide as the driving regent. The as-prepared graphene nanoscroll foam exhibits promising performance in… read more here.
Keywords: nitrogen doped; graphene nanoscroll; doped graphene; nanoscroll foam ... See more keywords
Machine Learning to Predict Binding Affinity.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9752-7_16
Abstract: Recent progress in the development of scientific libraries with machine-learning techniques paved the way for the implementation of integrated computational tools to predict ligand-binding affinity. The prediction of binding affinity uses the atomic coordinates of… read more here.
Keywords: machine; machine learning; learning techniques; binding affinity ... See more keywords
IConMHC: a deep learning convolutional neural network model to predict peptide and MHC-I binding affinity
Sign Up to like & getrecommendations! Published in 2020 at "Immunogenetics"
DOI: 10.1007/s00251-020-01163-9
Abstract: Tumor-specific neoantigens are mutated self-peptides presented by tumor cell major histocompatibility complex (MHC) molecules and are necessary to elicit host’s anti-cancer cytotoxic T cell responses. It could be specifically recognized by neoantigen-specific T cell receptors… read more here.
Keywords: peptide mhc; model; mhc binding; mhc ... See more keywords
The effects of mutation on the drug binding affinity of Neuraminidase: case study of Capsaicin using steered molecular dynamics simulation
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-021-05005-7
Abstract: The influenza virus is an important respiratory pathogen that causes many incidences of diseases and even death each year. One of the primary factors of this virus is the Neuraminidase surface protein, which causes the… read more here.
Keywords: steered molecular; using steered; affinity; drug ... See more keywords
Comparative cell uptake study of FITC-/177Lu-labeled RM26 monomer, dimer and trimer on PC-3: improving binding affinity of gastrin releasing peptide receptor (GRPR) antagonist via bivalency/trivalency
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Radioanalytical and Nuclear Chemistry"
DOI: 10.1007/s10967-018-6396-x
Abstract: The gastrin releasing peptide receptors (GRPRs) overexpress in various tumors, which provided the opportunity for GRPR targeted tumor radiological diagnosis and therapy. In recent reports, the GPPR antagonists presented superior specific targeting affinity over the… read more here.
Keywords: affinity; releasing peptide; dimer trimer; binding affinity ... See more keywords
Competitive binding affinity of two lanthanum(III) macrocycle complexes toward DNA and bovine serum albumin in water
Sign Up to like & getrecommendations! Published in 2017 at "Journal of the Iranian Chemical Society"
DOI: 10.1007/s13738-017-1172-3
Abstract: In the present study, two water-soluble lanthanum(III) hexaaza Schiff base complexes were synthesized and characterized and also theoretically investigated. The interactions of these complexes with DNA and bovine serum albumin (BSA) were studied using different… read more here.
Keywords: lanthanum iii; dna; dna bovine; binding affinity ... See more keywords