Software Directory

A single run of MDBNCH performs seven independent molecular dynamics calculations, using systems of different sizes and/or using different codes. The purpose of doing this is to sample a variety of different running conditions. MDBNCH results provide information about the speed of machines in classical molecular dynamics calculations using short-range potentials and neighbor lists. More generally, they may give you a feeling about the behavior of systems on codes which are relatively small, but tend to access memory in a quite irregular way, probably causing many cache misses on recent RISC architectures.

Set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD.

Media Gallery Pro, a goPro editor and MultiViewer capable of playing up to 6 HD movies simultaneously on a single display screen without additional hardware. Packed with robust features for audio visual editing, a powerful search functionality and movie/video indexing capabilities this is a must have software app that works well as a low end post production software suite. Media Gallery Pro also offers a full feature free 15 day trial available now. Edit your goPro movies, YouTube videos and more with this robust app for PC. Works great for creating sales presentations, trade show loops and point-of-sale scenarios for kiosks. Or, use as sports analysis tool capable of side by side movie and video playback for such things as perfecting golf swings. Download your copy and try MGP GoPro Editor/MultiViewer Video Player App. Or purchase the entire app for just $29.95USD and receive free updates for life.

Mercury offers a comprehensive range of tools for 3D structure visualization and the exploration of crystal packing. With a long pedigree and over 10,000 downloads, Mercury is firmly established as the visualiser of choice within the crystallographic community.

With a vast number of options for customizing display settings Mercury is widely used for the generation of publication-quality images. A Style Manager contains a number of pre-defined display styles for work, publication and presentation and also provides the ability to preserve and share your own custom display settings. Stunning 3D images created using Mercury can be exported in a variety of common formats. In addition, it is possible to render high quality ray-traced images using POV-Ray.

MetLigDB is a publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail

Crystallographic Programs for Microcomputers

Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination.

Determination of structural parameters of incommensurate one-dimensionally modulated structures by an automatic search routine on four-dimensional Fourier maps.

Information-calculating system on crystal structure data of minerals. Includes structure Database for Minerals and formation of the Calculated Powder X-ray Diffraction Standards (CPDS) Subbase and X-ray powder diffraction analytical techniques and crystal chemical analysis. Exists as stand-alone package or Internet access (see bibliography).

Macromolecular Crystallographic Information File

Python Macromolecular Library for the analysis and manipulation of macromolecular structural models

Program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling.

Homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled and MODELLER automatically calculates a model containing all non-hydrogen atoms. Implements comparative protein structure modeling by satisfaction of spatial restraints and can perform many additional tasks, including de novo modeling of oligopeptides, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

Yamamoto's software for modulated structures

Problems and Solutions. Software for Incommensurate/Modulated Structures

Molecular modelling from sequence analysis and alignment, multiple-structure alignment and superposition, remote homologue identification to 3D model building

Molecular modelling from sequence analysis and alignment, multiple-structure alignment and superposition, remote homologue identification to 3D model building

For identifying nonbonded interactions in small molecules and biomolecular structures. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it.

MoleCoolQt is a molecule viewer designed for experimental charge density studies with a user-friendly graphical user interface.

List of available software