Structural protein interactions: From months to minutes

Dafas, Panos; Gomoluch, Jacek; Kozlenkov, Alexander; Schroeder, Michael

doi:10.1016/s0927-5452(04)80084-4

Cited by 1 publication

(1 citation statement)

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“…Graph nodes represent amino acids, and edges are chosen in one of three ways: first, using a threshold for contact distance between residues; second, using Delaunay tessellation; and third, using the recently developed almostDelaunay edges. Furthermore, [9] presents a solution that reduced the computation of PSIMAP, a protein interaction map derived from protein structures in the protein databank PDB and the structural classification of proteins SCOP [10] to know about interaction of two proteins. The original PSIMAP algorithm computes all pair-wise atom/residue distances for each domain pair of each multi-domain PDB entry.…”

Section: Related Workmentioning

confidence: 99%

SimDiv: A New Solution for Protein Comparison

Sayyadi

Salehi

Ghodsi

2008

Lecture Notes in Electrical Engineering

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Proteins are the main players in the game of life. Good understanding of their structures, functions, and behaviors leads to good understanding of drugs, diseases, and thus our health. So, much effort has been done to study and categorize proteins. Nowadays, tens of thousands of proteins have been found. Moreover, the problem of comparing the proteins is hard. Therefore, efficient methods are needed to deal with this problem. In this paper, we use an important computational geometric concept and graph matching algorithm, namely, "Delaunay Tetrahedralization" and "Similarity Flooding", and propose a new idea to extract similar parts of proteins. Furthermore, we used protein fragmentation to reduce the time and storage complexity of the model for larger proteins. IntroductionThe number of known proteins is increasing every day; tens of thousands have been studied and categorized by now.To understand the functions and behaviors of a newly found protein, one should find well studied proteins with similar structure. In fact, the behavior of a protein is related to its sequence of amino acids and its 3D structure. So the comparison of proteins is a key technique not only in finding similarities in the structures of proteins but also to categorize them and define families and super-families among the proteins.

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Section: Related Workmentioning

confidence: 99%