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- Bala Krishnamoorthy, Alexander Tropsha
- Bioinformatics
- 2003

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)

- Christopher Deutsch, Bala Krishnamoorthy
- Bioinformatics
- 2007

MOTIVATION
There is a need for an efficient and accurate computational method to identify the effects of single- and multiple-residue mutations on the stability and reactivity of proteins. Such a method should ideally be consistent and yet applicable in a widespread manner, i.e. it should be applied to various proteins under the same parameter settings, and… (More)

- Tamal K. Dey, Anil N. Hirani, Bala Krishnamoorthy
- SIAM J. Comput.
- 2010

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)

- Bala Krishnamoorthy, Gábor Pataki
- Discrete Optimization
- 2009

We propose a very simple preconditioning method for integer programming feasibility problems: replacing the problem b ′ ≤ Ax ≤ b x ∈ Z n with b ′ ≤ (AU)y ≤ b y ∈ Z n , 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… (More)

- Bala Krishnamoorthy, Scott Provan, Alexander Tropsha
- 2005

We develop an objective characterization of protein structure based entirely on the geometry of its parts. The three-dimensional alpha complex filtration of the protein represented as a union of balls (one per residue) captures all the relevant information about the geometry and topology of the molecule. The neighborhood of a strand of contiguous alpha… (More)

- Bala Krishnamoorthy
- Oper. Res. Lett.
- 2008

Using a direct counting argument, we derive lower and upper bounds for the number of nodes enumerated by linear programming-based branch-and-bound (B&B) method to prove the infeasibility of an integer knapsack problem. We prove by example that the size of the B&B tree could be exponential in the worst case. 1 Introduction Linear programming-based… (More)

- Sharif Ibrahim, Bala Krishnamoorthy, Kevin R. Vixie
- JoCG
- 2013

We study the multiscale simplicial flat norm (MSFN) problem, which computes flat norm at various scales of sets defined as oriented subcomplexes of finite simplicial complexes in arbitrary dimensions. We show that the multiscale simplicial flat norm is NP-complete when homology is defined over integers. We cast the multiscale simplicial flat norm as an… (More)

- Ye Tian, Christopher Deutsch, Bala Krishnamoorthy
- Algorithms for Molecular Biology
- 2010

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)

- Tamal K. Dey, Anil N. Hirani, Bala Krishnamoorthy, Gavin Smith
- ArXiv
- 2013

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)

- Sharif Ibrahim, Bala Krishnamoorthy, Kevin R. Vixie
- JoCG
- 2016

Currents represent generalized surfaces studied in geometric measure theory. They range from relatively tame integral currents representing oriented compact manifolds with boundary and integer multi-plicities, to arbitrary elements of the dual space of differential forms. The flat norm provides a natural distance in the space of currents, and works by… (More)