akalpokas

akalpokas's Stars

• OpenBioSim/somd2

  SOMD2 molecular dynamics for free energy calculations

  Language:Python62

• yoheinakajima/instagraph

  Converts text input or URL into knowledge graph and displays

  Language:Python3.5k293

• OpenBioSim/biosimspace_tutorials

  A tutorials suite for BioSimSpace.

  Language:Jupyter Notebook155

• psi4/psi4

  Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

  Language:C++967446

• kamerlinlab/KIF

  KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.

  Language:Python232

• spack/spack

  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

  Language:Python4.3k2.3k

• choderalab/espaloma

  Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

  Language:Python21125

• noegroup/reform

  A simple implementation of replica exchange MD simulations for OpenMM.

  Language:Python222

• OpenFreeEnergy/gufe

  grand unified free energy by OpenFE

  Language:Python319

• matteoferla/Fragmenstein

  Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

  Language:Python18013

• choderalab/perses

  Experiments with expanded ensembles to explore chemical space

  Language:Python18151

• openmm/openmm

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

  Language:C++1.5k524

• MolSSI/cookiecutter-cms

  Python-centric Cookiecutter for Molecular Computational Chemistry Packages

  Language:Python38590

• luigibonati/mlcolvar

  A unified framework for machine learning collective variables for enhanced sampling simulations

  Language:Python8924

• openmm/openmm_workshops

  Language:Jupyter Notebook319

• microsoft/Graphormer

  Graphormer is a general-purpose deep learning backbone for molecular modeling.

  Language:Python2.1k336

• latex3/hyperref

  Hypertext support for LaTeX

  Language:TeX16837

• gto76/python-cheatsheet

  Comprehensive Python Cheatsheet

  Language:Python36.4k6.5k

• mamba-org/mamba

  The Fast Cross-Platform Package Manager

  Language:C++6.9k353

• proteneer/timemachine

  Differentiate all the things!

  Language:Python13817

• doyle-lab-ucla/auto-qchem

  Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

  Language:Python8818

• OpenBioSim/biosimspace

  An interoperable Python framework for biomolecular simulation.

  Language:Python7511

• alanwilter/acpype

  OFFICIAL: AnteChamber PYthon Parser interfacE

  Language:Python20347

• torvalds/linux

  Linux kernel source tree

  Language:C182k53.9k

• athityakumar/colorls

  A Ruby gem that beautifies the terminal's ls command, with color and font-awesome icons. :tada:

  Language:Ruby4.9k387

• OpenFreeEnergy/alchemiscale

  a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home

  Language:Python238

• Colvars/colvars

  Collective variables library for molecular simulation and analysis programs

  Language:C++20957

• biobootloader/wolverine

  Language:Python5.2k723

• Phlya/adjustText

  A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

  Language:Jupyter Notebook1.5k87

• OpenFreeEnergy/cinnabar

  Package for consistent reporting of relative free energy results

  Language:Python3713