Welcome to the Computational Biology Resources Read Me! In this curated collection, you will find a wealth of tools, databases, software packages, and resources tailored to support computational biologists and researchers in navigating the complexities of biological data analysis.
gitpod - Gitpod is a cloud development environment for teams to efficiently and securely develop software.
google colab - Colab is a hosted Jupyter Notebook service that requires no setup to use and provides free access to computing resources, including GPUs and TPUs.
kaggle - Kaggle is the world's largest data science community with powerful tools and resources to help you achieve your data science goals.
docker-builds - repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of programs
seqera containers - on-demand cointainers built
Awesome Nextflow - A curated list of Nextflow pipelines
nf-core - pipelines that are currently available as part of nf-core
IARC pipelines -International Agency for Research on Cancer bioinformatics platform pipelines
opentarget.org- freely-available, open source tool that highlights variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci, and identification of potential drug targets.
crispor - a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system
Tide - For non-templated Cas9 editing
Tider - For template-directed Cas9 editing
iSeq -iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
Gwak- data visualization tool in R
DEBrowser - Interactive Differential Expression Analysis Tool.
[bolt] (https://github.com/jwohlwend/boltz)
chai
alphafold - AlphaFold DB provides open access to over 200 million protein structure predictions to accelerate scientific research.
colabfold- Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding
cfold -contains a pipeline for predicting alternative conformations of protein structures.
Foldseek - Server offers fast and sensitive protein structure alignments against large protein structure collections.
protein-design tools repo -adaptvbio repo of protein design tools
Protein-Ligand Binding Database- The PLBD contains thermodynamic and kinetic data describing protein‑small molecule compound (ligand) interactions.
nuerosnap repo - repo for list of protein folding tools
chaidiscovery
EvolvePro
[DeepMutationalScanning]https://huggingface.co/spaces/thaidaev/zsp
RoseTTAFold2NA- RoseTTAFold2NA is an advanced computational tool developed to predict the structures of protein/nucleic acid complexes with high accuracy
Chroma-chroma is a generative model for designing proteins programmatically.## Epigenomic/Epigenome
UniFold-Alphafold in pytorch framework
ProteinX-Alphafold3 in pytorch framework
PyMOLFold
Protein Interaction- PIONEER: Generating whole-proteome human interactome using deep learning
SwissDrugSuite -suite of drug tools
admetlab- admet data
admet-ai
SyntheMol- Generative AI for Drug Discovery
RDKIT
OECHEM
polaris
DiffSBDD-Structure-based Drug Design with Equivariant Diffusion Models \