Search Results for "molecular docking software"
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Showing 274 open source projects for "molecular docking software"
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DockPanel Suite
The Visual Studio inspired docking library for .NET WinForms
Microsoft first introduced the docking panel layout in Visual Studio .NET (2002), and soon it became popular in application design. Many commercial .NET component vendors started to provide docking libraries initially, but there was no good free and open source alternative until WeiFen Luo released DockPanel Suite (DPS for short) on SourceForge.net in 2006. After an 18 month hiatus, the project has been resurrected and is now being actively developed on GitHub. -
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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 . ... -
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SASM
Simple crossplatform IDE for NASM, MASM, GAS and FASM languages
SASM (SimpleASM), simple Open Source crossplatform IDE for NASM, MASM, GAS, FASM assembly languages. SASM has syntax highlighting and debugger. The program works out of the box and is great for beginners to learn assembly language. SASM is translated into Russian, English, Turkish, Chinese, German, Italian, Polish, Hebrew, Spanish. In SASM you can easily develop and execute programs, written in NASM, MASM, GAS or FASM assembly languages. Enter code in form and simply run your program. In... -
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Docking-Affinity-Plotter
Docking Affinity Plotter: Visualize and analyze binding affinity data.
Docking Affinity Plotter: Visualize and analyze binding affinity data from molecular docking experiments. This desktop GUI tool allows researchers to load docking results, generate insightful plots, and create a PDF report. Features ✅ CSV File Loading: Accepts docking results with ligand names, binding affinity, RMSD upper bound (rmsd/ub), and RMSD lower bound (rmsd/lb) -
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LNPopupController
LNPopupController is a framework for presenting view controllers
LNPopupController is a framework for presenting view controllers as popups of other view controllers, much like the Apple Music and Podcasts apps. Once a popup bar is presented with a content view controller, the user can swipe or tap the popup bar at any point to present the popup. After finishing, the user dismisses the popup by either swiping or tapping the popup close button. The framework is intended to be very generic and work in most situations, so it is implemented as a category over... -
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AutoDockParser
A tool for efficient processing of Docking results
AutoDock Suit is one of the most popular software for performing Molecular Docking and Virtual Screening. This suit offers two programs AutoDock and AutoDock Vina. AutoDock provides its output as Docking Log Files (DLG files), while the latter outputs in pdbqt format. Post-processing of these results has long remained a manual job and hence various protocols and workflows are designed that are user-specific. -
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FairChem
FAIR Chemistry's library of machine learning methods for chemistry
FAIRChem is a unified library for machine learning in chemistry and materials, consolidating data, pretrained models, demos, and application code into a single, versioned toolkit. Version 2 modernizes the stack with a cleaner core package and breaking changes relative to V1, focusing on simpler installs and a stable API surface for production and research. The centerpiece models (e.g., UMA variants) plug directly into the ASE ecosystem via a FAIRChem calculator, so users can run relaxations,... -
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Hello ImGui
Hello, Dear ImGui: unleash your creativity in app development
hello_imgui is a cross-platform framework that simplifies the development of graphical applications using Dear ImGui. It abstracts away boilerplate code for window creation, input handling, and platform integration, allowing developers to focus on building user interfaces and interactive content quickly. Targeted at prototyping, tools, and GUI apps, hello_imgui works on Windows, macOS, Linux, iOS, and WebAssembly with minimal setup. Its plug-and-play nature makes it ideal for teaching,... -
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. ... -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of... -
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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in... -
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations", J. ... -
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LogD_Predictor
Models to LogD Predictor Software
The repository contains a packaged set of machine-learning models and neural networks for predicting logD from NMR spectra and molecular fingerprints. For more details, check the Github repository: https://github.com/Prospero1988/logD_predictor -
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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 anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. ... -
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ERmod
Approximate solvation free energy calculator
...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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GrowthRates
Calculate growth rates from microplate reader output
The Bellingham Research Institute (BRI) develops and distributes software that is free of charge to academic and other non-profit organizations. GrowthRates is our software tool that simplifies the analysis of microplate reader output from microbial growth experiments without having to program in Python, R, or MATLAB. It automates the calculation of growth rate parameters, including rates, lag times, maximum population density. Manual calculation of those parameters requires at least 5... -
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Win32++ is a C++ library used to build windows applications. It is a simple, open source alternative to MFC. Win32++ supports the C++ compilers from GNU and Microsoft. It is an ideal starting point for anyone learning to program for windows, but also caters for the needs of professional developers.
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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... -
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ASAF - Another Swing App Framework
an OSGi-based Swing Application Framework
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GeneMiner2 is based on our previously developed GeneMiner and Easy353 software and integrates excellent tools such as Blast, Minimap2, Fasttree, Muscle5, Mafft, Astral, PPD, PGA, NOVOPlasty, and OrthoFinder. Please cite the literature prompted by the software when using the corresponding functionalities. Our GeneMiner2 manuscript is currently under review: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y.
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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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NAMD-Automator
A GUI to automate Workflow for setting up and run NAMD simulations
Welcome to NAMD-Automator, a user-friendly graphical interface designed to simplify the process of Molecular Dynamics (MD) Simulation, by creating configuration files, and automate the simulation with simple form-based tabs. NAMD is one of the widely used software for running these simulations, known for its scalability, speed and efficiency with large molecular systems. However, setting up a typical simulation in NAMD usually requires crafting configuration file for each stage of a Conventional MD Simulation (CMD), such as Minimization, Heating, Equilibration and Production. ... -
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trilat-umn
Using FRET distances to trilaterate the location of a FRET acceptor
...This volumetric map is saved in MRC/CCP4-format, which can be displayed using common molecular graphics software. -
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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. atomes 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. ...
