Bala Krishnamoorthy

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MOTIVATION Most scoring functions used in protein fold recognition employ two-body (pseudo) potential energies. The use of higher-order terms may improve the performance of current algorithms. METHODS Proteins are represented by the side chain centroids of amino acids. Delaunay tessellation of this representation defines all sets of nearest neighbor(More)
Given a simplicial complex with weights on its simplices, and a nontrivial cycle on it, we are interested in finding the cycle with minimal weight which is homologous to the given one. Assuming that the homology is defined with integer (Z) coefficients, we show the following: <i>For a finite simplicial complex K of dimension greater than p, the boundary(More)
We propose a very simple preconditioning method for integer programming feasibility problems: replacing the problem b ≤ Ax ≤ b x ∈ Zn with b ≤ (AU)y ≤ b y ∈ Zn, where U is a unimodular matrix computed via basis reduction, to make the columns of AU short (i.e. have small Euclidean norm), and nearly orthogonal (see e.g. [20], [17]). Our approach is termed(More)
Circulating filarial proteins elicit strong immunologic reactions in humans leading to the chronic manifestations in human lymphatic filariasis such as lymphatic occlusion, fibrosis, edema, and in some cases, tropical pulmonary eosinophilia. Our earlier studies, in vitro, conclusively prove that filarial parasitic sheath proteins induce apoptosis in HEp2(More)
Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are(More)
We study the effect of edge contractions on simplicial homology because these contractions have turned out to be useful in various applications involving topology. It was observed previously that contracting edges that satisfy the so called link condition preserves homeomorphism in low dimensional complexes, and homotopy in general. But, checking the link(More)