Search Results for "molecule"
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Showing 43 open source projects for "molecule"
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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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RetroScheme- Get Your Retrosynthesis
- RetroScheme is used for molecule sketching and retrosynthesis
RetroScheme was specifically designed to help Chemists in knowing potential starting material through retrosynthetic analysis. The App is basically a GUI wrapper for the library Aizynthfinder from Astrazeneca.. - The App is coupled with molecular sketching tool to sketch your compound - This was made to be easy for the user and can be used endlessly to assist in potential new drug synthesis -
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MolPrep
RDkit-based Molecule Optimization Tool (CLI) in python.
MolPrep is a powerful utility application designed to streamline the preparation and refinement of molecular geometries. With the help of RDKit, this tool enables users to load, clean, standardize, and optimize molecular structures effortlessly. Its robust design ensures scalability and efficiency, making it ideal for chemoinformatics workflows. -
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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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Chem-Parser
Molecule Sketcher and Immediate Parser to Excel, .SMI and 3D SDF
Chem-Parser is an intuitive and efficient utility designed to streamline the data curation process for QSAR (Quantitative Structure–Activity Relationship) modeling and cheminformatics workflows. This versatile tool allows users to draw chemical structures, parse multiple SMILES strings, and automatically populate a structured table with associated compound names and custom-defined value tags such as biological activity or physicochemical properties. By enabling rapid structure-to-data... -
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rssfiz
Java science library.
Java science library. Project contains modules for physics units, particle and quantum physics, molecule, chemistry and universe definitions, also additional math classes. -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
...Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and... -
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Aestel
Applications for data management
...The reporting application provides a query builder and spreadsheet template designer. Both applications work with any relational data model. (Postgres and Oracle have been tested). The two applications have been initially developed for small molecule drug discovery research. However, they can be extended for use in other data domains. -
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A collection of codes that allow a user to store and use data on quantum levels in a system such as an atom, molecule, or nucleus.
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SMTracker (v1.5, v2.0)
A tool for analysis and visualization of single-molecule tracking data
SMTracker v2.0 is a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualising and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by- track basis. Diffusion parameters and motion behaviour is analysed by several methods: a) by a Gaussian mixture model ,or b) by using the cumulative probability distribution of square displacements, c) Mean-Squared... -
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LMAPper - The SPM and Mol Viewer
Where SPM images and molecular models meet
...It is useful to understand how your molecules fit to what you observed and can help interpret your data. What makes this application more useful than paint programs (powerpoint or inkscape) is the fact that the size of the images and of the molecule is fixed, so that you know that you are working in real space. Check https://sourceforge.net/p/spm-and-mol-viewer/wiki/Home/ for updates. -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
...These extensions allow to use of toolkits at all its grace and some features may be backported from others to introduce missing functionalities. Most important and handy property of Molecule in ODDT are Numpy dictionaries containing most properties of supplied molecule. Some of them are straightforward, other require some calculation, ie. atom features. Dictionaries are provided for major entities of molecules. -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. ... -
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Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
...Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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MoCalc2012
GUI for MOPAC, DFTB+, GAMESS, Firefly, NWChem, ORCA and PSI4
MoCalc2012 is a simple, efficient Graphical User Interface for MOPAC, DFTB+, GAMESS(US), Firefly, NWChem, ORCA and PSI4. -
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CRP - Chemical Reaction Prediction
Predicting Organic Reactions using Neural Networks.
The intend is to solve the forward-reaction prediction problem, where the reactants are known and the interest is in generating the reaction products using Deep learning. This Graphical User Interface takes simplified molecular-input line-entry system (SMILES) as an input and generates the product SMILE & molecule. Beam search is used in Version 2, to generate top 5 predictions. Maximum input length for the model is 15 (excluding spaces). -
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SMSD
SMSD is a Java based software library for calculating MCS.
SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure). -
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sdmixer
A tool for 2D/ 3D multi-color super resolution microscopy
The open source software sdmixer reconstructs a TIFF image from a single molecule localization data set. The spectral demixing option allows multi color super resolution microscopy. sdmixer supports multipage TIFF images and is able to process large 3D data sets. Further features are 2D/3D convolution, histogram based contrast enhancement and nearest neighbor analysis. -
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MS2Browser
LC-MS/MS data browser designed for siderophore analysis
...Some of the functionality and use of MS2Browser is described as part as an open-access book chapter: http://www.intechopen.com/books/applications-from-engineering-with-matlab-concepts/small-molecule-lc-ms-ms-fragmentation-data-analysis-and-application-to-siderophore-identification A siderophore structural database assembled for this project can be found alongside the MS2Browser software (.cfw format to be used with ChemBioFinder(TM) ). NOTE: The program is written for personal use to assist siderophore analysis using high-resolution LC-MS/MS data. ... -
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Nanopuller
AFM puller control software
Nanopuller by Konrad Pawlak and Janusz Strzelecki http://dx.doi.org/10.1016/j.ultramic.2016.01.008 http://www.biofizyka.fizyka.umk.pl/ Laboratory made AFM force spectroscopy setups were present in milestone single molecule experiments and there is a growing number of groups using such equipment even though the commercial setups are nowadays widely available. The ability to tailor the setup accordingly to particular application is an advantage that makes the effort necessary for construction a worthy investment. However, one advantage of using a commercial setup – repeatability and unification, cannot be archived, as every laboratory is developing a specific data acquisition protocol and software. ... -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. -
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An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges
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GUItars
GUItars is designed for the analysis of high throughput RNAi data.
Please refer to the original article published in PLOS ONE at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049386. GUItars's user-friendly graphical interface enables rapid analysis of RNAi and small molecule screens. GUItars uses SSMD for hit selection, which is preferred for its ability to diminish sample size effects and the false hit rate, making it superior to other widely used HTS analysis methods. The program can handle the analysis for screens without replicates as well as with replicates. For comparison purposes, non-SSMD-based methods such as percent activity, z-score, and t-test are also provided as scoring options. ...
