Search Results for "molecule"
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Showing 79 open source projects for "molecule"
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Ansible Molecule
Molecule aids in the development and testing of Ansible roles
Molecule project is designed to aid in the development and testing of Ansible roles. Molecule provides support for testing with multiple instances, operating systems and distributions, virtualization providers, test frameworks and testing scenarios. Molecule encourages an approach that results in consistently developed roles that are well-written, easily understood and maintained. Molecule supports only the latest two major versions of Ansible (N/N-1), meaning that if the latest version is 2.9... -
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Chemprop
Message Passing Neural Networks for Molecule Property Prediction
Chemprop is a repository containing message-passing neural networks for molecular property prediction. -
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MolecularGraph.jl
Graph-based molecule modeling toolkit for cheminformatics
MolecularGraph.jl is a graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia. -
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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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PreCompose
Compose Multiplatform Navigation && State Management
Compose Multiplatform Navigation && ViewModel, inspired by Jetpack Navigation, ViewModel and Lifecycle, PreCompose provides similar (or even the same) components for you but in Kotlin, and it's Kotlin Multiplatform project. -
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HomotopyContinuation.jl
A Julia package for solving systems of polynomials
.... An example of an non-algebraic objective function whose derivative is algebraic is the Kullback–Leibler divergence. Homotopy continuation methods allow us to study the conformation space of molecules as for example cyclooctane (CH₂)₈. This molecule consists of eight carbon atoms aligned in a ring, and eight hydrogen atoms, each of which is attached to one of the carbon atoms. -
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Ansible Role Jenkins
Ansible Role - Jenkins CI
This Ansible role automates the installation and initial configuration of Jenkins CI on servers running RHEL/CentOS or Debian/Ubuntu. It handles installation via package, ensures required tools like curl and Java 8+ are present, and is structured to integrate smoothly into repeatable provisioning workflows. Changes made to the Jenkins systemd override.conf file; the default set of changes set the configured URL prefix, Jenkins home directory, Jenkins port and adds the configured Jenkins and... -
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Chimerax-UCSF
ChimeraX is an application for visualizing and analyzing molecule
ChimeraX is an application for visualizing and analyzing molecule structures such as proteins, RNA, DNA, lipids as well as gene sequences, electron microscopy maps, X-ray maps, 3D light microscopy and 3D medical imaging scans. It is the successor of the UCSF Chimera program. Example images and feature highlights show a few of its capabilities, and recipes show example command and Python API use. -
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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. - Published in Wiley, Journal of Computational Chemistry . 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... -
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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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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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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
.... (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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Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
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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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Euler
A distributed graph deep learning framework.
As a general data structure with strong expressive ability, graphs can be used to describe many problems in the real world, such as user networks in social scenarios, user and commodity networks in e-commerce scenarios, communication networks in telecom scenarios, and transaction networks in financial scenarios. and drug molecule networks in medical scenarios, etc. Data in the fields of text, speech, and images is easier to process into a grid-like type of Euclidean space, which is suitable... -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
... and additional handles. 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
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. 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... -
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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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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
... of molecule-water complexes with graphical user interface (GUI), 2) semi-automatic frequency analysis using symbolic potential energy distribution matrix and comparison of optimized internal coordinates, 3) GUI for charge fitting with three modes: manual, Monte-Carlo sampling or brute force, and 4) GUI for dihedral terms fitting. The usage of these tools decreases the labor effort, lowers manual input errors and reduces the time needed for accurate MM parameterization efforts. -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
... 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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VividSTORM
Correlated confocal and SMLM data visualization and analysis
VividSTORM is a free and open-source standalone software with graphical user interface, for the correlated visualization and analysis of superresolution single molecule localization microscopy (SMLM) molecule lists and conventional pixel intensity-based images. The localization points (LPs) within this ROI can be analyzed using the selected built-in functions. NOTE: If you encounter issues not addressed by the user guide, please contact by message on this site or via e-mail for additional... -
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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).