brianjimenez
CTO at Zymvol. Software Engineer, PhD in bioinformatics, HPC and computational chemistry. I'm interested in building quality into scientific software.
@zymvol Barcelona
Pinned Repositories
ftdock-mpi
MPI parallel version of the FTDock protein-protein docking algorithm
kendrew
Yet another library for dealing with molecular and proteomic structures and information
protein-RNA-benchmark
pydock_tutorial
PyDock Tutorial
pygso
Python implementation of the Glowworm Swarm Optimization (GSO) algorithm.
python-course
Python course
rust-pdb
PDB toy parser in Rust language
lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
lightdock-python2.7
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
lightdock-rust
A Rust implementation of the LightDock macromolecular docking software
brianjimenez's Repositories
brianjimenez/pygso
Python implementation of the Glowworm Swarm Optimization (GSO) algorithm.
brianjimenez/python-course
Python course
brianjimenez/kendrew
Yet another library for dealing with molecular and proteomic structures and information
brianjimenez/FASPR
an ultra-fast, accurate and deterministic tool for protein side-chain packing
brianjimenez/surface-sampler
brianjimenez/eNES
Educational NES emulator in Rust
brianjimenez/Vina-GPU-2.0
Vina-GPU 2.0 accelerates AutoDock Vina and its related commonly derived docking methods, such as QuickVina 2 and QuickVina-W with GPUs.
brianjimenez/UDock2_nmrbox
brianjimenez/atm-cli
Command line tool for generating and working with MIDI files.
brianjimenez/brianjimenez
brianjimenez/brianjimenez.github.io
brianjimenez/chroma-pytorch
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
brianjimenez/ColabDesign
Making Protein Design accessible to all via Google Colab!
brianjimenez/coronavirus_structural_task_force
Repository for the molecular structures related with Corona virusses and their re-processing
brianjimenez/Diffusion_models_from_scratch
Creating a diffusion model from scratch in PyTorch to learn exactly how they work.
brianjimenez/foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
brianjimenez/Getting-Things-Done-with-Pytorch
Jupyter Notebook tutorials on solving real-world problems with Machine Learning & Deep Learning using PyTorch. Topics: Face detection with Detectron 2, Time Series anomaly detection with LSTM Autoencoders, Object Detection with YOLO v5, Build your first Neural Network, Time Series forecasting for Coronavirus daily cases, Sentiment Analysis with BERT.
brianjimenez/papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
brianjimenez/pdbe-api-training
Interactive Python notebooks for PDBe API training
brianjimenez/protein_scoring
Generating and scoring novel enzyme sequences with a variety of models and metrics
brianjimenez/ProteinMPNN
Code for the ProteinMPNN paper
brianjimenez/raytracing_1weekend
brianjimenez/RFDesign
Protein hallucination and inpainting with RoseTTAFold
brianjimenez/RFdiffusion
Code for running RFdiffusion
brianjimenez/rust-gso
A Rust implementation of the Glowworm Swarm Optimization algorithm
brianjimenez/trDesign
trRosetta for protein design
brianjimenez/UDock2_linux
brianjimenez/uoc_clase_16_04_2020
brianjimenez/vk_mini_path_tracer
A beginner-friendly Vulkan path tracing tutorial in under 300 lines of C++.
brianjimenez/wtfpython
Exploring Python through counter-intuitive snippets. If you think you know Python, think once more!