An adequate description of entire genomes has to include information on the three-dimensional (3D) structure of proteins. Most of these protein structures will be determined by high-throughput modeling procedures. Thus, a structure-based analysis of the network of protein-protein interactions in genomes requires docking methodologies that are capable of dealing with significant structural inacc...

Evolutionary approaches to molecular docking typically use a realvalue encoding with standard genetic operators. Mutation is usually based on Gaussian and Cauchy distributions whereas for crossover no special considerations are made. The choice of operators is important for an efficient algorithm for this problem. We investigate their effect by performing a locality, heritability and heuristic ...

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...

Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide f...

Protein kinase C (PKC) comprises a family of ubiquitous enzymes transducing signals by the lipophilic second messenger sn-1, 2-diacylglycerol (DAG). Teleocidin and its structurally simpler congener indolactam-V (ILV) bind to PKC with high affinity. In this paper, we report our computational docking studies on ILV binding to PKC using an automatic docking computer program, MCDOCK. In addition, w...

The GAAA tetraloop-receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the iso...

HDACs are important anticancer drug targets, and their study is currently being actively pursued. A series of HDAC inhibitors were docked to the homology models to understand the similarities and differences between the binding modes, docking analysis was applied to clarify the binding modes between the ligands and the receptor HDAC. The docking studies of some newly designed hydroxamate analog...

The combination of docking and molecular dynamics simulation is used to explain the isoform-specific selectivity between PI3Kalpha and PI3Kgamma, which are two lipid kinases in the class I PI3Ks. The protein flexibility is incorporated in docking the ligands to the ensemble of representative structures extracted from a clustering analysis of the molecular dynamics simulation in explicit aqueous...

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure a...

Visual haptic-based biomolecular docking systems could be used for both research and e-learning in research intensive disciplines such as biology, physical chemistry, molecular medicine, biophysics, structural biology, bioinformatics, etc. The assembly of molecules in a three-dimensional space or molecular docking is used for rational drug design where a ligand docks onto a receptor. The comput...