Albert Vilella's repositories
ThermoMPNN
GNN trained to predict changes in thermodynamic stability for protein point mutants
alphafold_non_docker
AlphaFold2 non-docker setup
apq-qsne
A collection of code for Dimensionality Reduction for Documents with Nearest Neighbor Queries
awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
bioSyntax
Syntax highlighting for computational biology
ColabDesign
Making Protein Design accessible to all via Google Colab!
dandelion
dandelion - A single cell BCR-seq analysis package for 10X Chromium 5' data
DProQ
Deep learning prediction of protein complex structure quality
enclone
VDJ Clone Analysis Tools
folding_tools
A collection of *fold* tools
GraphBP
Official implementation of "Generating 3D Molecules for Target Protein Binding" [ICML2022 Long Presentation]
k-means
Simple k-means clustering implementation
kmeans
Implementation of the K-Means clustering algorithm.
LMNglyPred
Prediction of Human N-Linked Glycosylation Site using embeddings from pre-trained protein language model
mark-nonconverted-reads
This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.
modPhred
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
nanoranger
simplified cellranger for long-read data
nf-bowtie
Align reads with bowtie to reference.
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
pline
JSON-based web interfaces for command-line programs
RDE-PPI
:mountain: Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)
SPACE2
Tool for rapid clustering of antibody models by the structure of their CDRs.
sword
tool for finding similar word in a file
Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies