Alzheimer’s disease (AD) as a complicated and progressive neurodegenerative disorder is the most common form of dementia and memory loss. On account of the multifactorial etiology of AD, the multi-target-directed ligand (MTDL) approach is a promising method in searching new drug candidates for this disease. Here, in this paper more than 500 tacrine-coumarin hybrids have been designed and drug-l...

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...

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...

  Objective(s): A fast and reliable evaluation of the binding energy from a single conformation of a molecular complex is an important practical task. Artificial neural networks (ANNs) are strong tools for predicting nonlinear functions which are used in this paper to predict binding energy. We proposed a structure that obtains binding energy using physicochemical molecular descripti...

Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general ap...

Contents 1. Introduction 1 1.

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