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...

MOTIVATION The limited success rate of protein-protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein-protein docking results and identify additional parameters that affect the performance of docking procedures. RESULTS We find that the distinction between nearly correct mo...

In this research work, a proficient method has been developed for the preparation of novel N-((2-chloroquinolin-3-yl) methylene)-4-methylbenzenamine derivatives from 2-chloroquinoline-3-carbaldehyde derivatives and p-toluidine in ethanol as solvent and using catalytic amount of acetic acid under reflux conditions to obtain desired products in good yields. The identification of all the synthesiz...

Govardhan A. Balaji, Vitukudi N. Balaji and Shashidhar N. Rao* Department of Chemistry, St Joseph’s College, 36 Langford Road, Bangalore 560 027, India Structure Directed Molecular Design, Jubilant Biosys Ltd, #96, Industrial Suburb II Stage, Yeshwantpur, Bangalore 560 022, India Tripos – A CertaraTM Company, 1699 South Hanley Road, St Louis MO 63144, USA Present address: Department of Chemistr...

abstract: objective(s): in recent years, the chemistry of 2-chloroquinoline-3-carbaldehydes have received considerable attention owing to their synthetic and effective biological importance which exhibits a wide variety of biological activity, n1,n4-bis((2-chloroquinolin-3-yl)methylene)benzene-1,4-diamine derivatives that synthesized from 2-chloroquinoline-3-carbaldehydes may have biological ef...

We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function predi...

We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexe...

We present a comprehensive molecular simulation program package, the Peking University Drug Design System (PKUDDS), which runs on personal computers. PKUDDS has been developed mainly for computer-aided drug design using the methods of two-dimensional quantitative structure-activity relationships, three-dimensional quantitative structure-activity relationships, molecular docking, and database sc...

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the ...

One pharmacophore model and three quantitative structure-activity relationship models were developed on a series of benzimidazole and imidazole inhibitors of histone deacetylase 2. The goodness of hit score value of the best pharmacophore model was 0.756, which indicated that it is reliable to be used for virtual screening. The built pharmacophore model was used to search the NCI database. The ...