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A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. It is a publicly(More)
Mutations that arise in HIV-1 protease after exposure to various HIV-1 protease inhibitors have proved to be a difficult aspect in the treatment of HIV. Mutations in the binding pocket of the protease can prevent the protease inhibitor from binding to the protein effectively. In the present study, the crystal structures of 68 HIV-1 proteases complexed with(More)
Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a beta-helical structure. Transition path(More)
In drug discovery and development, the conventional "single drug, single target" concept has been shifted to "single drug, multiple targets"--a concept coined as polypharmacology. For studies in this emerging field, dedicated and high-quality databases of multitargeting ligands would be exceedingly beneficial. To this end, we conducted a comprehensive(More)
Aberrant von Hippel Lindau (VHL) protein function is the underlying driver of VHL-related diseases, including both sporadic and inherited clear cell renal cell carcinoma (ccRCC). About one third of VHL mutations are missense point mutations, with R167Q being the most common VHL point mutation in hereditary VHL disease. Although it has been studied(More)
The present study develops a classification model to correlate the binding pockets of 70 HIV-1 protease crystal structures in terms of their structural descriptors to their complexed HIV-1 protease inhibitors. The Random Forest classification model is used to reduce the chemical descriptor space from 456 to the 12 most relevant descriptors based on the Gini(More)
A data mining study has been done using HIV-1 protease crystal structures complexed with FDA approved HIV-1 protease inhibitor drugs. Chemical descriptors have been computed for the binding pockets of each crystal structure, yielding approximately 600 constitutional, topological, geometric, elecrotostatic, and quantum mechanical descriptors for each(More)
A series of cyclic hydrocarbons analogs where a carbon displays unusual planar tetracoordinate structure is proposed, employing hybrid density functional theory calculations using B3LYP functional and 6-311+G** basis set. Various strategies were employed to design the neutral planar tetracoordinate hydrocarbon analogs. The same strategy is employed for(More)