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Towards protein folding by global energy optimization
Author(s) -
Abagyan Ruben A.
Publication year - 1993
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(93)81406-p
Subject(s) - protein folding , chemistry , biophysics , folding (dsp implementation) , computational biology , computer science , biochemistry , biology , engineering , electrical engineering
Different components of the theoretical protein folding problem are evaluated critically. It is argued that: (i) as a rule, small‐ and medium‐sized proteins are in the free energy minimum; (ii) long‐living metastable states may either appear occasionally with growing protein size, or be selected by evolution for a specific function; (iii) functions discriminating against incorrect folds would fail if they were used directly in the global optimization, unless they approximate the true free energy accurately; (iv) surface and electrostatic free energies should be treated separately; (v) confonnational entropy (of side chains in particular) should be taken into account; (vi) Monte Carlo procedures considering all free energy terms and combining global knowledge‐based random moves with local optimization have the largest potential for success.