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Predicting the helix packing of globular proteins by self‐correcting distance geometry
Author(s) -
Mumenthaler C.H.,
Braun W.
Publication year - 1995
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560040506
Subject(s) - globular protein , helix (gastropod) , protein secondary structure , geometry , topology (electrical circuits) , yield (engineering) , protein structure , sequence (biology) , globular cluster , crystallography , mathematics , physics , chemistry , combinatorics , biology , biochemistry , nuclear magnetic resonance , ecology , quantum mechanics , galaxy , snail , thermodynamics
Abstract A new self‐correcting distance geometry method for predicting the three‐dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 Å to 3.1 Å for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.