3d molecular modeling software download

This is the successor of WebLab Lite from Accelrys. WebLab Lite though is still available from some sites online. There are several advanced features on Discovery Studio Visualizer including the ability to show ligand binding sites in proteins and create a surface around the ligand. Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

It offers flexible high quality rendering and a powerful plugin architecture. Many consider this best for all platforms ArgusLab contains: An interactive 3D molecule builder that allows the user to build and manipulate complex structures; and, a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties.

The program is free for academic use. Mage requires the use of Kinemage files. There are presently available a large number of these files for both education and research purposes see the Kinemage Home Page for more information. You can now run Kinemages on your home page using a Java enabled Mage. Because of the large number of Kinemage files available to the public this makes for an interesting teacher tool.

See an example using the Mage Applet for the Fullerene Molecule. All in all, Ascalaph Designer is a great software to design molecular structures. Download it now. Download ArgusLab , a free chemistry drawing software and create different chemical models. Using this free chemistry software, you can draw the chemical structures of various compounds easily.

You can select any element to make a chemical structure from the built-in periodic table. All the atoms that you placed on your model are available on the left side of the software for easy access. In the Edit menu of the software, you will find an option named Auto Bonds. Enabling this feature will form chemical bonds among the atoms of a compound. By default, it forms the single bond between two atoms.

You can change single bond to double, triple, or hybrid bonds easily by right clicking on that bond. Moreover, various rendering options are available to represent a chemical structure.

Talking about hydrogen atoms, you can add all hydrogen atoms to the chemical structure with a single click. However, you can also add them one by one manually.

Besides this, you can also change the color of an atom. Each of the available calculations can be customized by setting values of different parameters. For convenience, some basic structures of rings and amino acids are provided in the software. You can use these structures directly in your molecular model. Following are some of the available structures:. MoluCAD is another free chemical drawing software to draw chemical models.

It lets you draw chemical structures in both 2D and 3D modes. Some commonly used elements to make a chemical structure are available on the right panel of the software. Other elements can be added to the chemical model from periodic table. You can launch the periodic table from the View menu. Four different views are available for each chemical structure, namely, top view, front view, side view, and oblique view. You can connect all atoms in a molecule with single, double, triple, or hybrid bonds.

Besides this, you can also change any atom or bond of a molecule by right-clicking on it. Render Modes : You will get more than 5 render modes to represent a chemical structure. MoluCAD comes with a large number of pre-designed molecular structures categorized in different folders:. You can animate your created chemical models. The animation will spin the molecular structures at a speed set by the user. While the animation is running, you can vary the speed of each axis of the molecular model separately.

Query is an important feature of MoluCAD. CheS-Mapper chemical space mapper. It embeds a dataset into 3D space by performing dimensionality reduction on the properties of the compounds. DataWarrior is a data visualization and analysis tool for chemical data with a rich set of available property calculations, similarity metrics, modeling capabilities, and data set representations.

DecoyFinder provides a GUI for selecting a set of decoy compounds from a large library that are appropriate matches to a given set of actives. Scaffold Hunter provides a Java-based GUI for visualizing the relationship between compounds in a dataset. 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. WCSE Wikipedia chemical structure explorer runs as a web application and provides a 2D interface for visualizing and searching for 2D molecules.

WebChemViewer is an online viewer for viewing and interacting with lists of compounds and their associated data. ABINIT also can optimize the geometry, perform molecular dynamics simulations, or generate dynamical matrices, Born effective charges, and dielectric tensors and many more properties. ACES performs calculations such as single point energy calculations, analytical gradients, and analytical Hessians, and is highly parallelized, including support for GPU computing. BigDFT performs ab initio calculations using Daubechies wavelets and has the capability to use a linear scaling method.

Periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions. CP2K performs simulations of solid state, liquid, molecular and biological systems. Its particular focus is massively parallel and linear scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics AIMD simulations. It is optimized for the mixed Gaussian and Plane-Waves method using pseudopotentials and can run on parallel and on GPUs.

Dacapo is a total energy program that uses density functional theory. ErgoSCM is a quantum chemistry program for large-scale self-consistent field calculations. It performs electronic structure calculations using Hartree-Fock and Kohn-Sham density functional theory and achieves linear scaling for both CPU usage and memory utilization.

ERKALE is designed to compute X-ray properties, such as ground-state electron momentum densities and Compton profiles, and core x-ray absorption and x-ray Raman scattering and valence electron excitation spectra of atoms and molecules. 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.

NWChem provides a full suite of methods for modeling both classical and QM systems. OpenMX Open source package for material eXplorer is designed for nano-scale material simulations based on DFT, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

OpenMX is capable of performing calculations of physical properties such as magnetic, dielectric, and electric transport properties and is optimized for large-scale parallelism. Psi4 is a suite of ab initio quantum chemistry programs that supports a wide range of computations e.

PyQuante is a collection of modules, mostly written in Python, for performing Hartree-Fock and DFT calculations with a focus on providing a well-engineered set of tools. It also has easy of use and extension as primary design goals. 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. Siam Quantum SQ is optimized for parallel computation and its capabilities include the calculation of Hartree-Fock and MP2 energies, minimum energy crossing point calculations, geometry optimization, population analysis, and quantum molecular dynamics.

FragIt generates fragments of large molecules to use as input files in quantum chemistry programs that support fragment based methods. It can extract grid-based quantities such as molecular orbitals and electron density, as well as Muliken population charges and other properties. Gabedit is a graphical user interface to a large number of quantum chemistry packages. It can create input files and graphically visualize calculation results. J-ICE is a Jmol-based viewer for crystallographic and electronic properties that can be deployed as a Java applet embedded in a web browser.

Campari conducts flexible Monte Carlo sampling of biopolymers in internal coordinate space, with built-in analysis routines to estimate structural properties and support for replica exchange and Wang-Landau sampling. Gromacs is a complete and well-established package for molecular dynamics simulations that provides high performance on both CPUs and GPUs.

MMTK Molecular Modelling Toolkit is a library written in Python with some time critical parts written in C for constructing and simulating molecular systems. Its capabilities include molecular dynamics, energy minimization, and normal mode analysis and it is well-suited for methods development. OpenMM is a substantial toolkit for high performance molecular dynamics simulations that includes support for GPU acceleration. ProtoMol , and the associated MDLab Python bindings , provides an object-oriented framework for prototyping algorithms for molecular dynamics simulations and includes an interface to OpenMM.

Sire is a collection of modular libraries intended to facilitate fast prototyping and the development of new algorithms for molecular simulation and molecular design. It has apps for system setup, simulation, and analysis. AmberTools is an open source component of the non-open source Amber package and provides a large suite of analysis programs.

As of Amber15, AmberTools includes the lower performance, but readily extendable, sander molecular dynamics code. MDAnalysis is a Python library for reading and analyzing molecular dynamics simulations with some time critical sections written in C. MDTraj provides high-performance reading, writing, and analysis of molecular dynamics trajectories in a diversity of formats from a Python interface.

MSMBuilder is an application and Python library for building Markov models of high-dimensional trajectory data. PDB2PQR prepares structures for electrostatics calculations by adding hydrogens, calculating sidechain pKa, adding missing heavy atoms, and assigning force field-dependent parameters; users can specify an ambient pH.

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. ProDy is a Python toolkit for analyzing proteins and includes facilities for trajectory analysis and druggability predictions using simulations of molecular probes. PyEMMA is a Python library for performing kinetic and thermodynamic analyses of molecular dynamics simulations using Markov models.

ACPC AutoCorrelation of Partial Charges computes ligand similarity based on a rotation and translation invariant electrostatic descriptor. Align-it TM is a successor of Pharao and aligns and scores 3D representations of molecules based on their pharmacophore features. It includes a plugin for integration with PyMOL. Pharmer uses efficient data structures to rapidly screen large libraries for ligand conformations that match a pharmacophore.