123 Open source projects that are alternatives of or similar to contact_map

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Structural Bioinformatics Training Workshop & Hackathon 2018

Notebook-integrated tools for molecular simulation and visualization

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Molecular simulation in Julia

Variational Autoencoder for Dimensionality Reduction of Time-Series

The ESPResSo package

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.

Modeling molecular ensembles with scalable data structures and parallel computing

Monte Carlo and Molecular Dynamics Simulation Package

😎 A curated list of awesome Molecular Dynamics libraries, tools and software.

Qball (also known as [email protected]) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.

Development version of plumed 2

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

Spatial alignment of single cell transcriptomic data.

Powerful, efficient particle trajectory analysis in scientific Python.

Comparison of active site and full kinase sequences for drug-target affinity prediction and molecular generation. Full paper: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00889

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

No description or website provided.

[email protected] COVID-19 efforts

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

a python package for the interfacial analysis of molecular simulations

Weighted Ensemble simulation framework in Python

A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.

Folding@home GPU benchmark

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

The chemistry library you were waiting for

Collection of scripts for bacterial genomics

pyiron - an integrated development environment (IDE) for computational materials science.

A curated list of awesome computational cryo-EM methods.

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

NequIP is a code for building E(3)-equivariant interatomic potentials

Ultrafast sequence typing and gene detection from NGS raw reads

Universal extensible molecular simulation engine

Physical validation of molecular simulations

🏗 Statistical models for biomolecular dynamics 🏗

Packmol - Initial configurations for molecular dynamics simulations

End-To-End Molecular Dynamics (MD) Engine using PyTorch

Molecular dynamics simulation software

Collective variables module for molecular simulation and analysis programs

Pytorch differentiable molecular dynamics

LOOS: a lightweight object-oriented structure analysis library

Tool to build force field input files for molecular simulation.

the simple alchemistry library

Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbour lists, etc.

Public development project of the LAMMPS MD software package

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

Unsupervised learning of atomic scale dynamics from molecular dynamics.

Quantum mechanic mass spectrometry calculation program

Syntax highlighting for computational biology

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

A Python library and command line interface for automated free energy calculations

OpenMM is a toolkit for molecular simulation using high performance GPU code.

Tensorflow + Molecules = TensorMol

Deep learning framework for data mining protein-protein interactions using CNN

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

CPM implementation in pure JavaScript

A Curated List of Computational Biology Datasets Suitable for Machine Learning