The purpose of the study was to compare the binding energy of pharmacophores of different classes targeting to kappa opioid receptor (KOR) with ketazocine and pentazocine which are having good activity on the KOR. The 3D structure of KOR receptor was built by Homology modeling; pharmacophores were characterized by using Ligand scout. Docking studies for the KOR agonists were performed in Autodo...

Results Homology modeling revealed that G432 forms part of a highly conserved structure motif (G/A/G/A) of small residues in homologous positions of all four domains (G432 (IS6), A780 (IIS6), G1193 (IIIS6), A1503 (IVS6)). In contrast, corresponding mutations in domains II, III and IV induced parallel shifts of activation and inactivation curves indicating a preserved coupling between both proce...

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures a...

A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic prediction...

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures a...

Background: Lipophosphoglycan 3 (LPG3) is required for the LPG assembly, a well known virulent molecule. In this study, the LPG3 gene of the lizard and mammalian Leishmania species were cloned and sequenced. A three-dimensional structure (3D) for the target sequence was also predicted by comparative (homology) modeling. Materials and Methods: An optimization PCR amplification was performed o...

We had participated in the CASP (Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction) that is the competition of the protein structure prediction in 2000 and 2002. Our server were estimated almost the best as the individual homology modeling server in the CAFASP3 (Critical Assessment of Fully Automated Structure Prediction) that is the full automa...

The current status of the protein prediction methods, comparative modeling, threading or fold recognition, and Ab Initio prediction, is described. The accuracy, applicability and shortcomings, as well as possible improvements will be discussed.

Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand dockin...