Track topics on Twitter Track topics that are important to you
The prediction of a ligand's binding mode into its macromolecular target is essential in structure-based drug discovery. Even though a tremendous effort has been made to address this problem, most of the tools developed work in a similar way, trying to predict the binding free energy associated with each particular binding mode. In this study we decided to abandon this criterium, following structural stability instead. This view, implemented in a novel computational workflow, quantifies the steepness of the local energy minimum associated to each potential binding mode. Surprisingly, the protocol outperforms docking scoring functions in case of fragments (ligands with MW < 300Da) and is as good as docking for drug-like molecules. It also identifies substructures that act as structural anchors, predicting their binding mode with particular accuracy. The results open a new physical perspective for binding mode prediction, which can be combined with existing thermodynamic-based approaches.
This article was published in the following journal.
Name: Journal of chemical information and modeling
Gordonia sp. IITR100 is a biodesulfurizing bacterium which can metabolize dibenzothiophene (DBT) to 2 hydroxybiphenyl in four steps via the 4S pathway. The genes involved in the metabolism are present...
Identification of correct protein-ligand binding poses is important in structure-based drug design and crucial for the evaluation of protein-ligand binding affinity. Protein-ligand coordinates are com...
The enzyme β-Ketoacyl ACP synthase I (KasA) is a potent drug target in mycolic acid pathway of Mycobacterium tuberculosis (Mtb). In the present study, we investigated the structural dynamics of wild-...
The postsynaptic density protein-95 (PSD-95) regulates synaptic plasticity through interactions mediated by its peptide binding PDZ domains. The two N-terminal PDZ domains of PSD-95 form an autonomous...
Adrenergic receptors are highly homologous while at the same time display a wide diversity of ligand and G-protein binding, and understanding this diversity is key for designing selective or biased dr...
With this project the investigators aim to investigate whether premature ventricular complexes (PVC) have a prognostic significance in persons without structural heart disease. Further the...
Heparin-Binding protein is a protein from primary and secretory granluae of white blood cells. It is released when white blood cells become activated and has been advocated as a biomarker ...
IL-22 is an IL-10 family cytokine that plays major actions to increase intestinal epithelial barrier function and regeneration during experimental colitis. IL-22 binding protein is a small...
Due to the widespread use of NGS, TTN is emerging as a major causative gene in neuromuscular disorders, with high clinical heterogeneity. The mechanisms underlying the phenotypic variabili...
The inflammatory bowel diseases represent a heterogeneous group of chronic , relapsing- inflammatory disorders of the gastrointestinal tract. Crohn's disease and ulcerative colitis are the...
A 513-kDa protein synthesized in the LIVER. It serves as the major structural protein of low-density lipoproteins (LIPOPROTEINS, LDL; LIPOPROTEINS, VLDL). It is the ligand for the LDL receptor (RECEPTORS, LDL) that promotes cellular binding and internalization of LDL particles.
A transmembrane-protein belonging to the TNF family of intercellular signaling proteins. It is a widely expressed ligand that activates APOPTOSIS by binding to TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTORS. The membrane-bound form of the protein can be cleaved by specific CYSTEINE ENDOPEPTIDASES to form a soluble ligand form.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
A nuclear receptor protein which in humans is encoded by the RARA gene. It belongs to a family of transcription regulators of ligand-responsive regulatory proteins which include steroid hormone receptors. In addition to a C-terminal ligand-binding domain, these nuclear receptors contain a highly-conserved N-terminal zinc-finger domain that mediates binding ligand-responsive elements.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Clinical Approvals Clinical Trials Drug Approvals Drug Delivery Drug Discovery Generics Drugs Prescription Drugs In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are dis...
Pharmacy is the science and technique of preparing as well as dispensing drugs and medicines. It is a health profession that links health sciences with chemical sciences and aims to ensure the safe and effective use of pharmaceutical drugs. The scope of...