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This project is aimed at providing useful thermodynamic tools for biochemists, including formation energy estimation of virtually every biochemical compound and metabolic pathway analysis and profiling.
FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
Cloud data warehouse to power your data-driven innovation
BigQuery is a serverless and cost-effective enterprise data warehouse that works across clouds and scales with your data.
BigQuery Studio provides a single, unified interface for all data practitioners of various coding skills to simplify analytics workflows from data ingestion and preparation to data exploration and visualization to ML model creation and use. It also allows you to use simple SQL to access Vertex AI foundational models directly inside BigQuery for text processing tasks, such as sentiment analysis, entity extraction, and many more without having to deal with specialized models.
SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE--
The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.
CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.
BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone.
Next-Gen Encryption for Post-Quantum Security | CLEAR by Quantum Knight
Lock Down Any Resource, Anywhere, Anytime
CLEAR by Quantum Knight is a FIPS-140-3 validated encryption SDK engineered for enterprises requiring top-tier security. Offering robust post-quantum cryptography, CLEAR secures files, streaming media, databases, and networks with ease across over 30 modern platforms. Its compact design, smaller than a single smartphone image, ensures maximum efficiency and low energy consumption.
The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.
DANGLE: A Bayesian inferential prediction method for protein backbone dihedral angles and secondary structure assignments, solely from sequence information, experimental chemical shifts and a database of known protein structures and their shifts.
Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
WebBabel is a python web application using OpenBabel to convert files
from one format to another.
It runs under Windows, Mac or Linux on your desktop, workstation or laptop.
It uses the Jmol (or Marvin) viewer to show the structures being converted.
easy to use sepctrography software. allow to display spectrography curves, and to overlay severals curves. you can create firste or second derivatives from the curves, or place marks to identify peaks.
finals drawings can be saved as png or pdf files.
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.
pyVib is a Python-based molecular graphics visualizer. It allows visualizing vibrational modes (from latest gaussian fchk files), the related IR/VCD/Raman/ROA spectra, the GCM's (group coupling matrices) and ACP's (atomic contribution patterns).
PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.