Papers in this group
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The design of biological active compounds from the apoenzyme is still a challenging task. Herein a simple yet efficient technique is reported to generate a receptor based pharmacophore solely using a ligand-free protein crystal structure. Human…
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Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching,…
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Molecular dynamics studies were performed on eight different crystal structure complexes of protein tyrosine phosphatase 1B (PTP1B) to study energy components and interactions important for the binding of substrates/inhibitors. Calculation of the…
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Protein kinase C (PKC) has been the center of many cell signaling pathways. PKC isoforms, specifically PKC-β II is linked to both diabetic complications as well as in promotion of angiogenesis and regulation of cancers. PKC-β II activates the…
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To prove the innate advantages of endogenous compounds/fragments for drug discovery and development, a novel index termed biological relevance (BR) is proposed. The results clearly indicate its ability to distinguish between synthetic chemicals,…
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To develop a new chemistry space filter with high efficiency and accuracy, an analysis on distributions of as many as 50 structural and physicochemical properties was carried out on both druglike and nondruglike databases, viz. MACCS-II Drug Data…
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Classification methods allow for the development of structure-activity relationship models when the target property is categorical rather than continuous. We describe a classification method which fits descriptor splines to activities, with…
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The application of the stochastic genetic algorithm (GA) in conjunction with the deterministic Powell search to analysis of the multicomponent powder EPR spectra based on computer simulation is described. This approach allows for automated…
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MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the…
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A seminar announcement system based on the extensive use of XML-based data structures, CML/MathML for carrying more domain-specific molecular content, and open source software components is described. The output is a resource description framework…
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There are several methods for virtual screening of databases of small organic compounds to find tight binders to a given protein target. Recent reviews in Drug Discovery Today have concentrated on screening by docking and by pharmacophore searching.…
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The dynamic nature and comparatively young age of computational chemistry is such that novel algorithms continue to be developed at a rapid pace. Such efforts are often wrought at the expense of extensive experimental validations of said techniques,…
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Target identification is a critical step following the discovery of small molecules that elicit a biological phenotype. The present work seeks to provide an in silico correlate of experimental target fishing technologies in order to rapidly fish out…
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In this paper, we describe the development of a set of integrated Web-based tools for mining the National Cancer Institute's (NCI) anticancer databases for anticancer drug discovery. For data mining, three different correlation algorithms were…