In this study, to accommodate receptor flexibility, based on multiple receptor conformations, a novel ensemble docking protocol was developed by using the naïve Bayesian classification technique, and it was evaluated in terms of the prediction accuracy of docking-based virtual screening (VS) of three important targets in the kinase family: ALK, CDK2, and VEGFR2. First, for each target, the repr...

In this work we have implemented and analyzed the performance of a new real coded steady-state genetic algorithm (SSGA) for the flexible ligand-receptor docking problem. The algorithm employs a grid-based methodology, considering the receptor rigid, and the GROMOS classical molecular force field to evaluate the energy function. In the implementation we used the restricted tournament selection (...

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...

The goal of this work was to determine if it is feasible to use Mir/Shuttle docking data to perform Mir damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify physical characteristics of a structure which can subsequently be used for damage detection. The RSS method was demonstrated for a nume...

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in an...

Various proteins play important roles in diabetes and a number of plants have been tested for their efficacy in modulating diabetes. Of all the proteins, we selected aloes reductase enzyme to analyze few plant compounds computationally for their efficacy towards protein inhibition. A total of 85 compounds from different parts of a plant, Cuminum cyminum were studied. Analysis was conducted usin...

conclusions rtesd in the prone position is safe and presents a feasible alternative for management of large rectal tumors. we also anticipate the technique to further improve with the advancement of robotic technology. introduction endoscopic submucosal dissection (esd) of large tumors of the rectum is particularly challenging using colonoscopy or with laparoscopic instruments. more recently ro...

Introduction:  Stereotactic  radiosurgery  is  a  technique  for  the  treatment  of  intracranial  lesions  with  highly  collimated  x-ray  beam.  Linac-based  radiosurgery  is  currently  performed  by  two  techniques:  couch or pedestal mounted. In the first technique, a device is required to affix patient's head to a couch  and  moreover  to  translate  it  accurately.  Structure  of  suc...

Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline....