نتایج جستجو برای: charmm

تعداد نتایج: 456  

Journal: :Comp. Opt. and Appl. 2011
Dexuan Xie Mazen G. Zarrouk

This paper gives a general convergence analysis to the truncated incomplete Hessian Newton method (T-IHN). It shows that T-IHN is globally convergent even with an indefinite incomplete Hessian matrix or an indefinite preconditioner, which may happen in practice. It also proves that when the T-IHN iterates are close enough to a minimum point, T-IHN has a Q-linear rate of convergence, and an admi...

Journal: :Molecules 2015
Dennis R Salahub Sergei Yu Noskov Bogdan Lev Rui Zhang Van Ngo Annick Goursot Patrizia Calaminici Andreas M Köster Aurelio Alvarez-Ibarra Daniel Mejía-Rodríguez Jan Řezáč Fabien Cailliez Aurélien de la Lande

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementat...

2003
Eugene Santos Keum Joo Kim Eunice E. Santos

We present a new and simple algorithmic approach to help predict protein structures from amino acid sequences based on energy minimization. In the search for the minimal energy conformation, we analyze and exploit the protein structures found at the various local minima to direct the search the global minimum. As such, we explore the energy landscape efficiently by considering only the space of...

2007
William S. Young Nicholas A. Nystrom Michael Schneider

To do its job, whatever it may be among the thousands of life-sustaining jobs proteins do, this dangly chain forged from hundreds of amino acids must fold into just the right threedimensional configuration. It happens within seconds, a long time in protein biochemistry, and the result is a complex bundle of twists and turns with clefts and notches precisely sculpted to allow the protein to atta...

Journal: :WIREs Computational Molecular Science 2011

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