written in C? CP2K performs simulations of solid state, liquid, molecular and biological systems. It is optimized for the mixed Gaussian and Plane-Waves method using pseudopotentials and can run on parallel and on GPUs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. Sire is a collection of modular libraries intended to facilitate fast prototyping and the development of new algorithms for molecular simulation and molecular design. MPQC (massively parallel quantum chemistry program) offers many features including closed shell, unrestricted and general restricted open shell Hartree-Fock energies and gradients, closed shell, unrestricted and general restricted open shell density functional theory energies and gradients, second order open shell perturbation theory and Z-averaged perturbation theory energies. Weka is a platform for data mining and machine learning that can be adapted for cheminformatics. These software let you draw the molecular structures of different chemical compounds. RMG is a DFT code that uses real space grids to provide high scalability across thousands of processors and GPU acceleration for both structural relaxation and molecular dynamics. The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. Fafoom (flexible algorithm for optimization of molecules) is a Python library for identifying low energy conformers using a genetic algorithm. Moreover, there are different styles to represent a chemical structure. PLIP (Protein-Ligand Interaction Profiler) runs as a web application and analyzes and visualizes protein-ligand interactions in 3D. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc. Avogadro is a 3D molecular viewer and editor with a modular plugin architecture with both Python and C++ bindings that includes interactive structure optimization for real-time editing. CWC (ChemDoodle Web Components) provides a suite of web-based visualizers and editors for 2D and 3D molecular data. VIDEAN (visual and interactive descriptor analysis) is a visual tool for iteratively choosing a subset of descriptors appropriate for predicting a target property with the aid of statistical methods. OpenMX is capable of performing calculations of physical properties such as magnetic, dielectric, and electric transport properties and is optimized for large-scale parallelism. ABC of cheminformatics by Filip Stefaniak. All in all, Ascalaph Designer is a great software to design molecular structures. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. Chem**f is a minimal cheminformatics toolkit written in the functional language Scala. Contribute to dkoes/Open-Source-Molecular-Modelling development by creating an account on GitHub. Cite. You can also vary the Van der Waals forces among atoms to 15%, 20%, 25%, etc. Chemozart is a WebGL-based web application for 3D editing of small molecules. Cross-Platform: Molecular builder/editor for Windows, Linux, and Mac OS X. ChemmineR is a cheminformatics package for the R statistical programming language that is built using Open Babel. ... Open Babel. MoluCAD comes with a large number of pre-designed molecular structures categorized in different folders: You can animate your created chemical models. PLUMED interfaces with an assortment of molecular dynamics software packages to provide a unified interface for performing free energy calculations using methods such as metadynamics, umbrella sampling and steered MD (Jarzynski). Free, open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications (hosts, i.e. Luscus is a 3D viewer and editor that is designed with a focus on electronic structure information. LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a highly modular classical molecular dynamics simulator that includes a diverse array of energy potentials and integrators. NCSA) are reported as BSD. qc-Programs, POV-Ray) by Jörg Dettmann. Its capabilities include SMARTS substructure search, descriptor calculation, and processing/filtering pipes. B KVFinder is a PyMOL plugin for identifying and characterizing pockets. PyRED generates RESP and ESP charges for the AMBER, CHARMM, OPLS, and Glycam and force fields. In order to launch the periodic table, you have to open the Free Drawing panel in the Build > Free drawing menu. PV (Protein Viewer) is a WebGL-accelerated viewer for interactive 3D visualization of macromolecules with a functional-style API. An intuitive molecular editor and visualization tool. Query is an important feature of MoluCAD. Pharmer uses efficient data structures to rapidly screen large libraries for ligand conformations that match a pharmacophore. Open3DALIGN performs unsupervised rigid-body molecular alignment. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. It computes 1875 descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints. In these molecular modeling software, you will find different styles to represent a chemical structure. or the Open Source Molecular Modeling updateable list of software. is a fully automated protein structure homology-modelling server, accessible via the Expasy web server, or from the program DeepView (Swiss Pdb-Viewer).. What is important for me is that it is open-source in a most conventional modern meaning and always being developed further and well-supported by the community. Ascalaph is a general purpose molecular modeling software that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. Open source, free to academics NWChem High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM/MM methods Open-source, Educational Community License version 2.0 ORAC A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level It can extract grid-based quantities such as molecular orbitals and electron density, as well as Muliken population charges and other properties. PocketPicker is a PyMOL plugin that automatically identifies potential ligand binding sites using a grid-based shape descriptor. VinaMPI is a wrapper for AutoDock Vina that uses OpenMPI to run large-scale virtual screens on a computing cluster. Chemtool is a 2D molecular editor for Linux systems that uses the GTK toolkit. AutoClickChem performs in silico click chemistry to generate large libraries of synthetically accessible compounds. PYTRAJ is a Python interface to the cpptraj tool of AmberTools. 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