Metabolites, 2022 Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay system that uses UHPLC-MS size-based separation methods to separate target-compound complexes from unbound compounds, identify bound compounds, classify compound binding sites ...
Thabo Ramatapa +5 more
doaj +1 more source
Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis [PDF]
, 2021 There is growing consensus that the optimization of the kinetic parameters for drug-protein binding leads to improved drug efficacy. Therefore, computational methods have been developed to predict kinetic rates and to derive quantitative structure ...
Ariane, Nunes Alves +3 more
core +1 more source
Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, 2021 Background: Mycobacterium tuberculosis protein target (DNA gyrase) is a type II topoisomerase target present in all bacteria. The enzyme comprises of two subunits A and B.
Gideon Adamu Shallangwa +1 more
doaj +1 more source
Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA) [PDF]
, 2013 The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage
Shen, Duanwen +15 more
core +2 more sources
Probing the interaction of the diarylquinoline TMC207 with its target mycobacterial ATP synthase. [PDF]
PLoS ONE, 2011 Infections with Mycobacterium tuberculosis are substantially increasing on a worldwide scale and new antibiotics are urgently needed to combat concomitantly emerging drug-resistant mycobacterial strains.
Anna C Haagsma +6 more
doaj +1 more source
Molecular simulations on proteins of biomedical interest : A. Ligand-protein hydration B. Cytochrome P450 2D6 and 2C9 C. Myelin associated glycoprotein (MAG) [PDF]
, 2011 TOPIC 1: Water molecules mediating polar interactions in ligand–protein complexes contribute to both binding affinity and specificity. To account for such water molecules in computer-aided drug discovery, we performed an extensive search in the Cambridge
Rossato, Gianluca
core +1 more source
SAM-DTA: a sequence-agnostic model for drug–target binding affinity prediction
Briefings in Bioinformatics, 2022 Abstract Drug–target binding affinity prediction is a fundamental task for drug discovery and has been studied for decades. Most methods follow the canonical paradigm that processes the inputs of the protein (target) and the ligand (drug) separately and then combines them together. In this study we demonstrate, surprisingly, that a model
Zhiqiang Hu +9 more
openaire +2 more sources
Sequence-based drug-target affinity prediction using weighted graph neural networks
BMC Genomics, 2022 Background Affinity prediction between molecule and protein is an important step of virtual screening, which is usually called drug-target affinity (DTA) prediction. Its accuracy directly influences the progress of drug development.
Mingjian Jiang +5 more
doaj +1 more source
Structural insights and therapeutic targets in Acinetobacter baumannii capsule biosynthesis
FEBS Letters, EarlyView.Hypervirulent KL49 A. baumannii's capsular polysaccharide contains the nonulosonic acid 8‐epi‐Leg5,7Ac2, synthesized by epimerization via ElaA, ElaB, and ElaC. Crystal structures of ElaA, ElaB, and ElaC reveal their role in CMP‐Leg5,7Ac2 synthesis and regioselective C8 epimerization.
Woo Cheol Lee +7 more
wiley +1 more source
Dipeptide Frequency of Word Frequency and Graph Convolutional Networks for DTA Prediction
Frontiers in Bioengineering and Biotechnology, 2020 Deep learning is an effective method to capture drug-target binding affinity, but low accuracy is still an obstacle to be overcome. Thus, we propose a novel predictor for drug-target binding affinity based on dipeptide frequency of word frequency ...
Xianfang Wang +6 more
doaj +1 more source