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Protein tertiary structure prediction using a branch and bound algorithm
Author(s) -
Eyrich Volker A.,
Standley Daron M.,
Felts Anthony K.,
Friesner Richard A.
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19990401)35:1<41::aid-prot5>3.0.co;2-n
Subject(s) - dihedral angle , van der waals force , algorithm , root mean square , protein tertiary structure , beta (programming language) , sequence (biology) , protein structure prediction , ranging , set (abstract data type) , mathematics , protein structure , computer science , chemistry , physics , molecule , quantum mechanics , telecommunications , programming language , hydrogen bond , biochemistry
Abstract We report a new method for predicting protein tertiary structure from sequence and secondary structure information. The predictions result from global optimization of a potential energy function, including van der Waals, hydrophobic, and excluded volume terms. The optimization algorithm, which is based on the αBB method developed by Floudas and coworkers (Costas and Floudas, J Chem Phys 1994;100:1247–1261), uses a reduced model of the protein and is implemented in both distance and dihedral angle space, enabling a side‐by‐side comparison of methodologies. For a set of eight small proteins, representing the three basic types—all α, all β, and mixed α/β—the algorithm locates low‐energy native‐like structures (less than 6Å root mean square deviation from the native coordinates) starting from an unfolded state. Serial and parallel implementations of this methodology are discussed. Proteins 1999;35:41–57. © 1999 Wiley‐Liss, Inc.