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Protein-Protein Interaction Databases
2015Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions of research are explored.
Szklarczyk, Damian, Jensen, Lars Juhl
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Compression of protein sequence databases
Bioinformatics, 1995We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information ...
Victor B. Strelets, Hwa A. Lim
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Protein design with fragment databases
Current Opinion in Structural Biology, 2011Structure-based computational methods are popular tools for designing proteins and interactions between proteins because they provide the necessary insight and details required for rational engineering. Here, we first argue that large-scale databases of fragments contain a discrete but complete set of building blocks that can be used to design ...
Erik, Verschueren +5 more
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Databases of Protein–Protein Interactions and Complexes
2009In the current understanding, translation of genomic sequences into proteins is the most important path for realization of genome information. In exercising their intended function, proteins work together through various forms of direct (physical) or indirect interaction mechanisms.
Hong Sain, Ooi +5 more
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Searching the protein sequence database
Bulletin of Mathematical Biology, 1984As the volume of protein sequence data grows, rapid methods for searching the protein sequence database become of primary importance. Rigorous comparison of sequences is obtained with the well-known dynamic programming algorithms. However, these algorithms are not rapid enough to use for routinely searching the entire database. In this paper we discuss
B C, Orcutt, W C, Barker
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Protein Function Database as a Deductive and Object-Oriented Database
1991This paper describes an experiment on a knowledge base approach to molecular biological databases, especially focusing on a protein function database.
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Software and Databases for Protein–Protein Docking
Protein-protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed.Małgorzata, Jarończyk +2 more
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Protein Superfamily Database (Prosup)
1996We have constructed a protein superfamily database (PROSUP). Amino acid sequences belonging to the protein superfamilies defined by PIR International are quantified by application of principal component analysis on the basis of the physicochemical properties of amino acid residues.
Katsuhisa Horimoto +3 more
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Mechanisms, regulation and functions of the unfolded protein response
Nature Reviews Molecular Cell Biology, 2020Claudio Hetz +2 more
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