Protein–DNA recognition: Breaking the combinatorial barrier

Autor:	Richard Lavery, Krystyna Zakrzewska, Cyril Deremble
Rok vydání:	2008
Předmět:	HMG-box Base pair General Physics and Astronomy Computational biology Plasma protein binding Bioinformatics DNA sequencing DNA binding site chemistry.chemical_compound chemistry Hardware and Architecture Binding site DNA Binding domain
Zdroj:	Computer Physics Communications. 179:112-119
ISSN:	0010-4655
DOI:	10.1016/j.cpc.2008.01.033
Popis:	We have developed a computational methodology that aims at predicting the binding sites of proteins on DNA. The crucial point of the methodology is to enable the protein binding energies to be calculated for very large numbers of DNA sequences (>1080) in a reasonable amount of computer time. In contrast to an earlier approach, we take into account both DNA and protein flexibility during the calculations. The speed-up comes from dividing the optimization into sub-problems involving overlapping DNA fragments, several nucleotide pairs in length, with associated protein fragments. Each optimization provides energies that can be added together to reconstitute the total binding energy of the protein for any chosen base sequence. We describe this new methodology and carry out some preliminary tests on biologically relevant proteins and protein complexes.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_________::2789b45b877f800b2f3c6d7f77dd4491 https://doi.org/10.1016/j.cpc.2008.01.033 Zobrazit plný text záznamu Full Text from ScienceDirect