3-d molecular modeling software

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.

Pharmit is a successor of Pharmer that also incorporates shape matching and energy minimization if a receptor structure is available as part of the screen. MolView is a modeling software for chemistry with a quite different interface than the other packages mentioned above. Its main difference consists in the fact that it is a free and online web-application.

It is a very easy program to use, even if you have no prior experience in kind of 3D modeling software. This Open-Source web-application can be used both as molecular editor and as a 3D model viewer. With MolView, apart from creating structural formulas, you can also use it for protein display, modeling and simulation of proteins assembly and Chain representation. But keep in mind that the free version of ChemSketch does not include all the features of the commercial version.

However, it is a pretty complete software that can be used for educational purposes, either by high school students or by undergraduate chemistry students. With this software, you can draw organic chemical structures, structures of organometallics, polymers and Markush structures. As a user, you are also given the possibility of calculating molecular properties, such as molecular weight, density, molar refractivity etc.. It is also possible to preview your 2D molecular design in 3D to visualize better the designed structure.

If you are interested in getting familiar with molecular modeling software for chemistry, you will eventually find the one that suits you best. From software related to 3D modeling and simulation of chemical structures to simulation packages, the market has many options to offer you.

Moreover, if you enjoy reading about chemistry, we propose you to go through this blog post, about 3D printing for the chemical industry. We hope you find this collection of software for chemistry useful. If you want to always get the most updated news about the latest modeling suites and software tools, subscribe to our newsletter to receive the latest news related to technology. Subscribe to our weekly newsletter to hear about the latest 3D printing technologies, applications, materials, and software.

Forgot your password? Don't have an account? Register now. Connect with Google. Connect with Facebook. Sign Up. To know more about how Sculpteo processes your personal information, you can check the privacy policy. 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. It lets you calculate the distance between two atoms, bond length, bending angle, torsion angle, total mass of the cluster , etc. It saves the project in its own supported MCD file format. If I talk about the basic features, you can do the following with a chemical model:.

It also lets you change the geometry of a chemical model by inflating or deflating the atoms. The properties of atom and the scene content are available on the screen. Moreover, it also has an auto-rotate button, clicking on which the molecular models starts rotating.

Jmol is an open source molecular modeling software based on JAVA. It does not have many advanced features as compared to other molecular modeling software in this list, but still, it is a good molecular modeling software.

You can easily create chemical structures of different compounds. Moreover, adding or changing bonds in a chemical compound is not a difficult task. Some commonly used elements carbon, oxygen, hydrogen, nitrogen, fluorine, chlorine, etc. If your chemical model requires elements other than the available ones, you need to add them manually by writing their symbol, say Zn for Zinc.

You can add a maximum of 9 elements for each chemical compound. The unavailability of the periodic table in the software makes it quite unstable for molecular modeling. Multiple views are provided for a model: top, left, right, bottom, and front. Besides this, viewing at different axes option is also available.

Talking about bonds, you can display bonds in single wireframe structure or adjust their width as 0. The measurement tool lets you measure the distance between two atoms in a molecule.

The measured distance is displayed in nanometer, Angstroms, and picometers. You can increase or decrease the bond distance by dragging an atom.