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Fragment-based Molecular Expansion

Python 20 2 Updated Jan 11, 2024

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Python 141 9 Updated Jan 2, 2025

A framework for text-guided protein design

Python 21 4 Updated Feb 21, 2025

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Jupyter Notebook 539 157 Updated Aug 12, 2024

Codes for our paper "Full-Atom Peptide Design with Geometric Latent Diffusion" (NeurIPS 2024)

Python 43 2 Updated Feb 6, 2025

C-library for calculating Solvent Accessible Surface Areas

C 126 36 Updated May 27, 2024

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Jupyter Notebook 330 46 Updated Jan 13, 2025

Standardized data set for machine learning of protein structure

Python 883 131 Updated Nov 18, 2020

AlphaFold 3 inference pipeline.

Python 6,104 751 Updated Feb 24, 2025

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

C++ 1,026 459 Updated Feb 14, 2025

Plugin for folding sequences directly in PyMOL

Jupyter Notebook 84 16 Updated Feb 11, 2025

A Euclidean diffusion model for structure-based drug design.

Python 393 89 Updated Feb 24, 2025

a package to simulate fluid surfaces and biomembranes

C++ 30 9 Updated Dec 6, 2024

Official repository for the Boltz-1 biomolecular interaction model

Python 1,595 213 Updated Feb 24, 2025

Software for the prediction of DEER and PRE data from conformational ensembles.

Jupyter Notebook 12 3 Updated Sep 3, 2024

A trainable PyTorch reproduction of AlphaFold 3.

Python 941 88 Updated Feb 20, 2025

In silico directed evolution of peptide binders with AlphaFold

Jupyter Notebook 145 31 Updated Jan 30, 2025

The Rosetta Bio-macromolecule modeling package.

C++ 214 74 Updated Feb 8, 2025

Codes and scripts for "An artificial intelligence accelerated virtual screening platform for drug discovery"

Jupyter Notebook 47 8 Updated Dec 16, 2024

User friendly and accurate binder design pipeline

Python 449 89 Updated Jan 2, 2025

Chai-1, SOTA model for biomolecular structure prediction

Python 1,544 199 Updated Feb 24, 2025

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some t…

TeX 113 19 Updated Dec 29, 2018

Official repository for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

Python 77 9 Updated Feb 22, 2025

Template-based protein design with Raygun

Python 56 6 Updated Nov 4, 2024

This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user examples are also available.

Jupyter Notebook 35 2 Updated Nov 20, 2024

Official Repository for the Uni-Mol Series Methods

Python 786 134 Updated Feb 25, 2025

Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.

Python 14 Updated Jul 17, 2024

Protein structure diffusion model for unconditional protein generation and motif scaffolding

Python 139 22 Updated Jun 24, 2024

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Python 2,905 569 Updated Feb 24, 2025
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