[A new program complex EFOLD for molecular modeling: the use of a flexible weighting coefficient scheme and the standard valence geometry in modeling the enzyme active sites].
An algorithm for the representation of biopolymer structures in an internal coordinate system (so-called structure regularization) by minimizing the target function with a flexible weighting coefficient scheme using three components that determine the reliability of deviations of each atom was proposed. For the structure regularization, an algorithm for taking into account the temperature factor was suggested for the first time. It was shown by the example of the aspartyl protease rhizopuspepsin that the representation in the internal coordinate system may result in an accurate reproduction of the structural details of separate molecule fragments, such as the active site region of the enzyme. This algorithm was realized as one of the modules of our EFOLD program complex. The English version of the paper.
Ruzheĭnikov
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SN
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia.
Popov
M E
ME
Kashparov
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D001224:Aspartic Acid / Q000737:chemistry; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry / Q000378:metabolism; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D005998:Glycine; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation; D012984:Software; D013696:Temperature
D004798:Enzymes; D001224:Aspartic Acid; D016282:Aspartic Acid Endopeptidases; C035794:rhizopuspepsin; D005998:Glycine