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af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

aimnet2

allosteric-pathways

Building and analyzing residue interaction networks with cofactors (includes tutorial).

alphamissense_db_search

Jupyter notebook script to search on the AlphaMissense database.

amber-cloud-image-bakery

A repository for building VM images for Amber and AmberTools for use with public cloud providers.

amber-membrane_protein_tutorial

Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen

amber_scripts

asciimol

Curses based ASCII molecule viewer for linux terminals.

awesome-programming-for-kids

A curated list of resources for teaching kids programming.

bien-249

Materials for the BIE249

bien135

Materials for the BIEN135

bien165

Materials for the BIEN165 class

biocolabs

a collection of colabs useful for molecular biology

biomolecular-structures-analysis

Scripts to help scientists on analysis of 3D biomolecular structures or molecular dynamics simulations trajectories

biopandas

Working with molecular structures in pandas DataFrames

calculatepartialchargeswithpsi4

An example Jupyter Notebook for calculating partial charges using Psi4

chem101.6

cloud-bind

Cloud-based Drug Binding Structure Prediction

colab-db.github.io

Repository of Jupyter Notebooks on Colab, Binder and Huggingface for Bio, Chemistry and Physics

colabfold

Making Protein folding accessible to all via Google Colab!

condacolab

Install Conda and friends on Google Colab, easily

confid

ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories

deep-learning-with-python-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

delfta

Δ-QML for medicinal chemistry

dipole-charges-calculator

Least-Squares fit solution for the adjustment of charges while keeping the total dipole moment of a molecule.

egb_2023

Simulações de Dinâmica Molecular em Nuvem (Making it Rain)

equibind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

exmol

Explainer for black box models that predict molecule properties

gamd-openmm

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/