13 citations · 15 across the 7 of their papers we have counts for
8 papers
Accelerator Codesign as Non-Linear Optimization
Nirmal Prajapati, Sanjay Rajopadhye, Hristo Djidjev +3
We propose an optimization approach for determining both hardware and software parameters for the efficient implementation of a (family of) applications called dense stencil comput…
CSA: Comprehensive comparison of pairwise protein structure alignments
Inken Wohlers, Noël Malod-Dognin, Rumen Andonov +1
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heurist…
Algorithm engineering for optimal alignment of protein structure distance matrices
Inken Wohlers, Rumen Andonov, Gunnar W. Klau
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-res…
Maximum Cliques in Protein Structure Comparison
Noël Malod-Dognin, Rumen Andonov, Nicola Yanev
Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can…
Solving Maximum Clique Problem for Protein Structure Similarity
Noël Malod-Dognin, Rumen Andonov, Nicola Yanev
A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same…
Towards Structural Classification of Proteins based on Contact Map Overlap
Rumen Andonov, Nicola Yanev, Noël Malod-Dognin
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained…