There are questions concerning the functions of artemin, an abundant stress protein found in Artemiaduring embryo development. It has been reported that artemin binds RNA at high temperatures in vitro, suggesting an RNA protective role. In this study, we investigated the possibility of the presence of RNA-bindingsites and their structural properties in artemin, using docking energy ...

Protein recognition is one of the most challenging and intriguing problems in structural biology. Despite all the available structural, sequence and biophysical information about protein-protein complexes, the physico-chemical patterns, if any, that make a protein surface likely to be involved in protein-protein interactions, remain elusive. Here, we apply protein docking simulations and analys...

Studies of intermolecular energy landscapes are important for understanding protein association and adequate modeling of protein interactions. Landscape representation at different resolutions can be used for the refinement of docking predictions and detection of macro characteristics, like the binding funnel. A representative set of protein-protein complexes was used to systematically map the ...

Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligand-protein systems by a combined thermodynamic and kinetic analysis of the binding energy landscapes. Misdocked predictions in ligand-protein docking are classified as 'soft' and 'hard' failures. While a soft failure arises when the search algorithm is unable to find the global energy min...

monoamine oxidase (ec, 1.4.3.4) or amine oxidoreductase catalyzes the oxidative deamination of biogenic amines. abnormal action of the monoamine oxidase b has been associated with neurological dysfunctions including parkinson´s disorder. monoamine oxidase b inhibitors divulged that these agents were effective in the therapeutic management of parkinson's disease. understanding the interaction of...

objective(s): a fast and reliable evaluation of the binding energy from a single conformation of a molecular complex is an important practical task. artificial neural networks (anns) are strong tools for predicting nonlinear functions which are used in this paper to predict binding energy. we proposed a structure that obtains binding energy using physicochemical molecular descriptions of the se...

human immunodeficiency virus infection / acquired immunodeficiency syndrome (hiv/aids) is a disease pertained to the human immune system. given its crucial role in viral replication, hiv-1 protease (hiv-1 pr) is a prime therapeutic target in aids therapy. in this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in hiv-1 pr in...

objective(s): recently, phthalimide derivatives were designed based on ameltolide and thalidomide as they possess a similar degree of anticonvulsant potency due to their phenytoin-like profile. the ability of phthalimide pharmacophore to interact with neuronal voltage-dependent sodium channels was studied in the batrachotoxin affinity assay. therefore, in the present study, a series of 19 compo...

the antidiuretic effect of arginine vasopressin (avp) is mediated by the vasopressin v2 receptor. the docking study of avp as a ligand to v2 receptor helps in identifying important amino acid residues that might be involved in avp binding for predicting the lowest free energy state of the protein complex. whereas previous researchers were not able to detect the exact site of the ligand-receptor...