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openmm_runner

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

openrxn

A free, open-source tool for modeling chemical reaction networks in Python

openseekr

OpenSEEKR is an extension of the SEEKR suit of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory.

opensmarts

Open Standard for the SMARTS chemical query language (Extends OpenSMILES)

opensmiles

The OpenSMILES specification

opensmog

OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.

opensmokepp_kineticoptimizer

Optimization of kinetic parameters of reactions included in a detailed kinetic mechanism

opensourcemolecularmodeling.github.io

Catalog of Open Source Molecular Modeling Projects

openssl

OpenSSL bindings for R

opensysgen

A tool for systematic conformer generation

opentox-toxcast

ToxCast database exposed throgh an OpenTox API • http://toxcast-api.cloud.douglasconnect.com/beta/ui/

opentsne

Extensible, parallel implementations of t-SNE

openvaccine-covid-19-mrna-vaccine-degradation-

We are designing a model using CNN+GCN to predict the likely degradation rates at each base of an RNA molecule, trained on a subset of an Eterna dataset comprising over 3000 RNA molecules (which span a panoply of sequences and structures) and their degradation rates at each position. We will then score our models on a second generation of RNA sequences that have just been devised by Eterna players for COVID-19 mRNA vaccines.

openworkstation

An open source and modular workstation concept for life science automation

openxlsx

openxlsx - a fast way to read and write complex xslx files

openxlsx2

openxlsx2 - read, write and modify xlsx files

opera

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

operaws

Web service wrapper for OPERA - a free and open source QSAR tool for predicting physicochemical properties and environmental fate endpoints

opp-op-pop-init

PyPI package containing opposition learning operators and population initializers for evolutionary algorithms

oppr

Prioritize conservation projects for funding

ops-crs

ops-knime

Project for integration of OPS and the Knime workflow engine

optedr

Calculated optimal designs for single variable models with the cocktail algorithm

optical-chemical-structure-recognition

Input- hand-drawn image of molecule... Output- SMILES format molecule name

optimization

optimization_protein-solubility

It uses optimisation algorithms to maximise protein solubility with constrained mutation to protein sequence.

optimizer

Unified Framework for Numerical Optimizer in R

optimizt

CLI image optimization tool

optimol

Optimization of binding affinities in chemical space for drug discovery