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Publications (5)9.93 Total impact

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    ABSTRACT: Familial hypertrophic cardiomyopathy (FHC) is a Mendelian disorder usually caused by mutations in any one of more than 12 genes, most of which encode sarcomere proteins. The disease exhibits extensive genetic heterogeneity, and it is important to identify mutations that result in adverse symptoms and/or lethality in affected individuals. An analysis of disease-causing mutations has been initiated in the Indian population to determine prevalent mutations. FHC was detected using echocardiography and by analysis of clinical symptoms and family history. The disease-causing mutation was identified using polymerase chain reaction DNA sequencing. The p.R787H mutation was identified in the MYH7 gene in two FHC families. Sequence and structure analysis suggested impaired binding of the mutant protein to the myosin essential light chain. Although the mutation results in variable clinical symptoms in the affected individuals, probably owing to the effect of modifier genes and/or environmental factors, it does not appear to be a lethal mutation.
    Experimental and clinical cardiology 01/2010; 15(1):e1-4. · 1.10 Impact Factor
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    ABSTRACT: Steroid 21-hydroxylase deficiency is the most common cause of congenital adrenal hyperplasia (CAH). Detection of underlying mutations in CYP21A2 gene encoding steroid 21-hydroxylase enzyme is helpful both for confirmation of diagnosis and management of CAH patients. Here we report a novel 9-bp insertion in CYP21A2 gene and its structural and functional consequences on P450c21 protein by molecular modeling and molecular dynamics simulations methods. A 30-day-old child was referred to our laboratory for molecular diagnosis of CAH. Sequencing of the entire CYP21A2 gene revealed a novel insertion (duplication) of 9-bp in exon 2 of one allele and a well-known mutation I172N in exon 4 of other allele. Molecular modeling and simulation studies were carried out to understand the plausible structural and functional implications caused by the novel mutation. Insertion of the nine bases in exon 2 resulted in addition of three valine residues at codon 71 of the P450c21 protein. Molecular dynamics simulations revealed that the mutant exhibits a faster unfolding kinetics and an overall destabilization of the structure due to the triple valine insertion was also observed. The novel 9-bp insertion in exon 2 of CYP21A2 genesignificantly lowers the structural stability of P450c21 thereby leading to the probable loss of its function.
    Journal of Biomedical Science 02/2009; 16:3. · 2.46 Impact Factor
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    ABSTRACT: Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.
    Bioinformatics 01/2008; 23(24):3320-7. · 5.47 Impact Factor
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    ABSTRACT: BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration) The NMITLI-BioSuite Team* Keywords: Bioinformatics, BioSuite, industry–academia collaboration, software. THE last decade has witnessed an exponential growth of information in the field of biological macromolecules such as proteins and nucleic acids and their interactions with other molecules. Computational analysis and predictions based on such information are increasingly becoming an essential and integral part of modern biology. With rapid advances in the area, there is a growing need to develop versatile bioinformatics software packages, which are effi-cient and incorporate the latest developments in this field. In view of this, the Council of Scientific and Industrial Research, India, undertook an initiative to promote a unique industry–academia collaboration, to develop a compre-hensive bioinformatics software package, under its New Millennium Initiative for Technology Leadership in India programme. BioSuite, a product of that effort, has been developed by Tata Consultancy Services who took the primary coding responsibility with significant backing from a large academic community who participated on advisory roles through the project period. BioSuite integrates the functions of macromolecular sequence and structural analysis, chemoinformatics and algorithms for aiding drug discovery. The suite organized into four major modules, contains 79 different programs, making it one of the few comprehensive suites that caters to a major part of the spectrum of bioinformatics applica-tions. The four major modules, (a) Genome and proteome sequence analysis, (b) 3D modelling and structural analysis, (c) Molecular dynamics simulations and (d) Drug design, are made available through a convenient graphics-user in-terface along with adequate documentation and tutorials. The unique partnership with academia has also ensured that the best available methodology has been adopted for each of the 79 programs, which has been thoroughly evaluated in several stages, leading to high scientific value of the suite. The software, apart from having the advantage of running on a Linux platform on a personal computer, is also flexible, modular, and allows for newer algorithms to be plugged into the overall framework. The package will be valuable for high quality academic research, industrial research and development and for teaching purposes, both locally within the country as well as in the international arena.
    Current science 01/2007; 92(1):29-38. · 0.91 Impact Factor
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    ABSTRACT: BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration) The NMITLI-BioSuite Team* Keywords: Bioinformatics, BioSuite, industry–academia collaboration, software. THE last decade has witnessed an exponential growth of information in the field of biological macromolecules such as proteins and nucleic acids and their interactions with other molecules. Computational analysis and predictions based on such information are increasingly becoming an essential and integral part of modern biology. With rapid advances in the area, there is a growing need to develop versatile bioinformatics software packages, which are effi-cient and incorporate the latest developments in this field. In view of this, the Council of Scientific and Industrial Research, India, undertook an initiative to promote a unique industry–academia collaboration, to develop a compre-hensive bioinformatics software package, under its New Millennium Initiative for Technology Leadership in India programme. BioSuite, a product of that effort, has been developed by Tata Consultancy Services who took the primary coding responsibility with significant backing from a large academic community who participated on advisory roles through the project period. BioSuite integrates the functions of macromolecular sequence and structural analysis, chemoinformatics and algorithms for aiding drug discovery. The suite organized into four major modules, contains 79 different programs, making it one of the few comprehensive suites that caters to a major part of the spectrum of bioinformatics applica-tions. The four major modules, (a) Genome and proteome sequence analysis, (b) 3D modelling and structural analysis, (c) Molecular dynamics simulations and (d) Drug design, are made available through a convenient graphics-user in-terface along with adequate documentation and tutorials. The unique partnership with academia has also ensured that the best available methodology has been adopted for each of the 79 programs, which has been thoroughly evaluated in several stages, leading to high scientific value of the suite. The software, apart from having the advantage of running on a Linux platform on a personal computer, is also flexible, modular, and allows for newer algorithms to be plugged into the overall framework. The package will be valuable for high quality academic research, industrial research and development and for teaching purposes, both locally within the country as well as in the international arena.