DebiChem Molecular Modelling packages

Авогадро је систем молекуларне графике и моделирања намењен молекулима и биомолекулима. Може да прикаже својства као што су орбите молекула или електростатички потенцијали а одликује га спознатљив изграђивач молекула.

У особености спадају:

• Уобличавач молекула са самосталним прилагођавањем геометрије на основу силе поља
• Механика молекула која укључује ограничења и претраге сагласности
• Приказивање орбита молекула и опште исо-површине
• Приказивање вибрација и исцртавање вибрационог спектра
• Подршка кристалографских поља јединице
• Стварање улаза за пакете Гаусове, ГАМЕС и МОЛПРО квантне хемије
• Прилагодљива архитектура прикључка и писање скрипти у Питону

У записе датотека које Авогадро може да чита спадају ПДБ, ХУЗ, ЦМЛ, ЦИФ, Молден, као и Гаусов, ГАМЕС-ов и МОЛПРО излаз.

BALLView provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

BALLView can be considered a graphical user interface on the basis of BALL (Biochemical Algorithms Library) with a focus on the most common demands of protein chemists and biophysicists in particular. It is developed in the groups of Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen, Germany). BALL is an application framework in C++ that has been specifically designed for rapid software development in Molecular Modeling and Computational Molecular Biology. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications.

OpenStructure aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

ProMod3 is a modelling engine based on the OpenStructure computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms.

PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

• Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
• Molecular builder and sculptor
• Internal raytracer and movie generator
• Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

nMOLDYN is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.