effects of partial docking on feedlot performance and body fat characteristics were studied in a fat-tailed sheep breed. thirty-eight male lambs with an average weight of 4.44 ± 0.48 were randomly divided into two groups. the lambs in one group were partially docked at 3-4 h after birth, using rubber rings, and the lambs in another group remained intact (control). after weaning, 20 male lambs f...

Plasmodium falciparum alanine M1-aminopeptidase (PfA-M1) is a validated target for anti-malarial drug development. Presence of significant similarity between PfA-M1 and human M1-aminopeptidases, particularly within regions of enzyme active site leads to problem of non-specificity and off-target binding for known aminopeptidase inhibitors. Molecular docking based in silico screening approach for...

he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages ov...

With the rapid development of computational techniques and hardware, more rigorous and precise theoretical models have been used to predict the binding affinities of a large number of small molecules to biomolecules. By employing continuum solvation models, the MM/GBSA and MM/PBSA methodologies achieve a good balance between low computational cost and reasonable prediction accuracy. In this stu...

The results of cognate docking with the prepared Astex dataset provided by the organizers of the "Docking and Scoring: A Review of Docking Programs" session at the 241st ACS national meeting are presented. The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of th...

modeling and simulation techniques are now widely used alongside with their experimental counterparts in order to complement them, or sometimes to bring first insights into the possible outcome of experiments. “modeling” is a general word that could encompass a wide range of methods that could be applied to a variety of subjects and problems. here, the use of selected molecular modeling methods...

The complex formed by the hairpin ribozyme and its substrate consists of two independently folding domains which interact to form a catalytic structure. Fluorescence resonance energy transfer methods permit us to study reversible transitions of the complex between open and closed forms. Results indicate that docking of the domains is required for both the cleavage and ligation reactions. Dockin...

Epstein-Barr Virus (EBV) infects a large percentage of the world’s population and is responsible for infectious mononucleosis and, in rare cases, Burkitt’s lymphoma and nasopharyngeal carcinoma. EBV’s primary means of infection is the association of the viral surface glycoprotein gp350 with Complement Receptor 2 (CR2) of the immune system. Various mutagenesis studies have identified key residue...

The urgent need for novel HIV-1-RT inhibitors with broad spectrum chemotherapeutic properties has provided an impetus for understanding the structural requisites of HIV-1-RT inhibitors at the molecular level. Toward this objective, binding mode analysis of 113 benzimidazole analogs was performed. First, molecular docking studies were performed on novel benzimidazoles by Glide program in the act...

The anti-ESBL activity of 1, 2-benzenedicarboxylic acid, mono (2-ethylhexyl) ester (DMEHE) extracted from marine Streptomyces sp strain VITSJK8 was further confirmed by in silico analysis. A total of 10 ESBL proteins was chosen for this study from the protein data bank (PDB) and were docked with the DMEHE. The resultant atomic contact energy (ACE) was compared with dockings of known antibiotic ...