نتایج جستجو برای: charmm

تعداد نتایج: 456  

2008
Sunhwan Jo Miklós Vargyas Judit Vasko-Szedlar Benoît Roux Wonpil Im

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calcu...

2009
Yunqi Li Ambrish Roy Yang Zhang

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms...

Journal: :Journal of chemical theory and computation 2011
H Lee Woodcock Benjamin T Miller Milan Hodoscek Asim Okur Joseph D Larkin Jay W Ponder Bernard R Brooks

The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling pack...

Journal: :Journal of Computational Chemistry 1998
Michal Vieth Jonathan D. Hirst Brian N. Dominy Heidi Daigler Charles L. Brooks

Ž . ABSTRACT: We assess the efficiency of molecular dynamics MD , Monte Ž . Ž . Carlo MC , and genetic algorithms GA for docking five representative ligand]receptor complexes. All three algorithms employ a modified CHARMM-based energy function. The algorithms are also compared with an established docking algorithm, AutoDock. The receptors are kept rigid while flexibility of ligands is permitted...

Journal: :Journal of computational chemistry 2009
Alexey Aleksandrov Thomas Simonson

Tetracyclines (Tcs) are an important family of antibiotics that bind to the ribosome and several proteins. To model Tc interactions with protein and RNA, we have developed a molecular mechanics force field for 12 tetracyclines, consistent with the CHARMM force field. We considered each Tc variant in its zwitterionic tautomer, with and without a bound Mg(2+). We used structures from the Cambridg...

Journal: :Journal of computational chemistry 2007
H. Lee Woodcock Milan Hodoscek Andrew T. B. Gilbert Peter M. W. Gill Henry F. Schaefer Bernard R. Brooks

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are power...

1998
R. Das J. Saltz

This paper is concerned with the implementation of the molecular dynamics code, CHARMM, on massively parallel distributed-memory computer architectures using a data-parallel approach. The implementation is carried out by creating a set of software tools, which provide an interface between the parallelization issues and the sequential code. Large practical MD problems is solved on the Intel iPSC...

نمودار تعداد نتایج جستجو در هر سال

با کلیک روی نمودار نتایج را به سال انتشار فیلتر کنید