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
Binding, thermodynamics, and selectivity of a non-peptide antagonist to the melanocortin-4 receptor [PDF]
, 2018 The melanocortin-4 receptor (MC4R) is a potential drug target for treatment of obesity, anxiety, depression, and sexual dysfunction. Crystal structures for MC4R are not yet available, which has hindered successful structure-based drug design.
Clark, Timothy +5 more
core +2 more sources
ChemBoost: A chemical language based approach for protein-ligand binding affinity prediction
, 2020 Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences.
Ozkirimli, Elif +3 more
core +1 more source
Funnel metadynamics as accurate binding free-energy method [PDF]
, 2013 A detailed description of the events ruling ligand/protein interac- tion and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have de- veloped a metadynamics-based approach, named funnel
LIMONGELLI, VITTORIO +2 more
core +1 more source
Site-Directed Mutagenesis and Site-Specific Binding Analysis of Calmodulin (CaM) [PDF]
, 2017 Calcium signaling is a major regulatory system in cells and a crucial part of cell biology. An important element in the decoding of intracellular calcium concentration into downstream processes is the ubiquitous and highly conserved calcium binding ...
Dokic, Yelena
core +1 more source
Fragments and hot spots in drug discovery [PDF]
, 2015 R01 GM064700 - NIGMS NIH HHSPublished ...
Kozakov, Dima +2 more
core +2 more sources
Computational structure‐based drug design: Predicting target flexibility [PDF]
, 2018 The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early
Ding X. +4 more
core +2 more sources
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
Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows [PDF]
, 2017 We describe a computational protocol to aid the design of small molecule and peptide drugs that target protein-protein interactions, particularly for anti-cancer therapy. To achieve this goal, we explore multiple strategies, including finding binding hot
A Goncearenco +44 more
core +1 more source