乐胖代购免代理版

{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T08:29:19Z","timestamp":1723451359778},"reference-count":35,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2008,11,20]],"date-time":"2008-11-20T00:00:00Z","timestamp":1227139200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2009,7,15]]},"abstract":"Abstract<\/jats:title>We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient\u2010based energy minimization of molecular complexes using this representation suffers from well\u2010known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient\u2010based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well\u2010defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non\u2010differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem, 2009<\/jats:p>","DOI":"10.1002\/jcc.21159","type":"journal-article","created":{"date-parts":[[2008,11,20]],"date-time":"2008-11-20T20:06:35Z","timestamp":1227211595000},"page":"1371-1378","source":"Crossref","is-referenced-by-count":11,"title":["A new method for the gradient\u2010based optimization of molecular 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