Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

The MolScript program produces publication-quality images of macromolecular 3D structures.

G-T/U mismatch dynamics in RNA-DNA hybrids

The PERL scripts are developed to search regions carring short motif within a long reference sequence.

End-to-end RNA Design using deep reinforcement learning

Code used to generate figures in the RLSuite paper

List of Geometric GNNs for 3D atomic systems

Basic RNA 3D structure comparison metrics in RNA-Puzzles, including INF, DI and RMSD. It also includes `RNA_normalizer` tool in pdb_utils.

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Working with molecular structures in pandas DataFrames

Example data files from the wwPDB for expansion of the CCD identifier length to greater than three characters

RNAView identifies base pairs that are formed in nucleic acid structures and classifies them according to the system of Leontis and Westhof

CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

Make changes to FMHY

Python code to run Supervised Molecular Dynamics (SuMD) simulations

diffpdb - a simple tool to compare text-content of PDB files

awesome tools for RNA

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

Companion webpage to the book "Mathematics For Machine Learning"

This introduces a suggestion of mathematical notation protocol for machine learning.

Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 500 universities from 70 countries including Stanford, MIT, Harvard, and Cambridge.

Dictionary extension that helps you stay focused on what you are reading by eliminating the need to search for meaning.

LOOS: a lightweight object-oriented structure analysis library

Repository containing all the Python materials

Contacts-based classifier of biological and crystallographic interfaces

an ultra-fast, accurate and deterministic tool for protein side-chain packing

Analyse Nucleic Acids Structure and Simulations with baRNAba

Contacts-based classifier of biological and crystallographic interfaces