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X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
TLDR
This manual to X-PLOR Version 3.1 presents the theoretical background, syntax and function of the programme and also provides a comprehensive list of references and sample input files with comments.Abstract:
X-PLOR is a highly sophisticated computer program that provides an interface between theoretical foundations and experimental data in structural biology, with specific emphasis on X-ray crystallography and nuclear magnetic resonance spectroscopy in solution of large biological macro-molecules. This manual to X-PLOR Version 3.1 presents the theoretical background, syntax, and function of the program and also provides a comprehensive list of references and sample input files with comments. It is intended primarily for researchers and students in the fields of computational chemistry, structural biology, and computational molecular biology.read more
Citations
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Journal ArticleDOI
Features and development of Coot.
TL;DR: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models and the current state of development and available features are presented.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
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AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
TL;DR: The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR, and their outputs include a detailed breakdown of the restraint violations.
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VESTA: a three-dimensional visualization system for electronic and structural analysis
Koichi Momma,Fujio Izumi +1 more
TL;DR: VESTA as mentioned in this paper is a cross-platform program for visualizing both structural and volumetric data in multiple windows with tabs, including isosurfaces, bird's-eye views and two-dimensional maps.
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SUPERFLIP– a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions
Lukáš Palatinus,Gervais Chapuis +1 more
TL;DR: SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm and has been successfully compiled and tested on a variety of operating systems.
References
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Journal ArticleDOI
Optimization by Simulated Annealing
TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
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Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
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Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.