Search Results for "molecular chemistry"
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Showing 291 open source projects for "molecular chemistry"
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DeepChem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, etc
DeepChem aims to provide a high-quality open-source toolchain that democratizes the use of deep learning in drug discovery, materials science, quantum chemistry, and biology. DeepChem currently supports Python 3.7 through 3.9 and requires these packages on any condition. DeepChem has a number of "soft" requirements. If you face some errors like ImportError: This class requires XXXX, you may need to install some packages. Deepchem provides support for TensorFlow, PyTorch, JAX and each requires... -
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smina
Scoring and Minimization with AutoDock Vina
A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. -
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Molsketch
2D molecule editor
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. -
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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vmdStore
vmdStore provides a user-friendly interface to free install VMD plugin
vmdStore provides a user-friendly interface to free install VMD plugins. vmdStore also helps you keeping the plugins always updated. Minimum Requirements Operating System: macOS, Linux, or Windows Visual Molecular Dynamics (VMD) 1.9.3 or later -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
...", J. Chem. Theory Comput. 11 (2015), 2517-2524 L.C.Kröger, W.A.Kopp, M.Döntgen, K.Leonhard, "Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations", J. Chem. Theory Comput. 13 (2017), 3955-3960 M.Döntgen, F.Schmalz, W.A.Kopp, L.C.Kröger, K.Leonhard, "Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations", J. Chem. Inf. Model. 58 (2018), 1343-1355 Check the Wiki for bug reports and fixes. -
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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JSmol
JavaScript-Based Molecular Viewer From Jmol
JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app. It can be used in conjunction with the Java applet to provide an alternative to Java when the platform does not support that (iPhone/iPad) or does not support applets (Android). Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet platforms... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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OSRA is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD file format- a computer recognizable molecular structure You can find links to the binary executables here: https://sourceforge.net/p/osra/wiki/Download/
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Developed with Synchronized functioning of Python and Batch scripts - Compatible on Windows - Accepted on Journal of Computational Chemistry - DOI: 10.1002/jcc.27390 -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Combinatorial Molecule Generation - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact... -
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pharmit
Open-source online virtual screening tools for large databases
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KryoMol
A molecular viewer for quantum chemistry files
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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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ERmod
Approximate solvation free energy calculator
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method (J. Chem. Phys. 113, 6070 (2000)). The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER. -
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Atomes
Analysis, visualization, edition of 3D atomistic models
Atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. Atoms is a toolbox developed to analyze, to visualize and to create/edit three-dimensional atomistic models. Atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K Atomes is developed by Dr. Sébastien Le Roux... -
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bmrblib
The BMRB library
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format. -
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ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can... -
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almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
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WavePacket (C++/Python)
Time-dependent simulation of open and closed quantum systems
... or chemistry. WavePacket is suitable for teaching quantum mechanics as well as for research projects in physics and chemistry. The present C++ version is an object-oriented rewrite of the existing Matlab version aiming to be more flexible. In particular, the goals are easy handling of open and closed systems and support for unusual setups. -
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Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.
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MSCC Applications Support
Materials and Computational Chemistry applications on HPC platform
Five software i.e. AMDKIIT , ANN-CI, LITESOPH, MTASpec, and µ2mech are developed as an outcome of the Materials and Computational Chemistry (MSCC) project under the National Supercomputing Mission (NSM). These are the set of codes (software) developed by the investigators to perform the computations to study the properties of atoms, molecules, clusters, alloys, bio-molecules, and composite materials using high-performance computing (HPC). For more information on the softwares developed under...