Artificial Intelligence

alphafold

alphafold is an artificial intelligence program developed by Google DeepMind that predicts the 3D structure of proteins directly from their amino acid sequences.

alphapulldown

alphapulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer

deepqmc

deepqmc implements variational quantum Monte Carlo for electrons in molecules, using deep neural networks written in PyTorch as trial wave functions. Besides the core functionality, it contains implementations of the PauliNet.

diann

diann - a universal software suite for data-independent acquisition (DIA) proteomics data processing. Conceived at the University of Cambridge, UK, in the laboratory of Kathryn Lilley (Cambridge Centre for Proteomics), DIA-NN opened a new chapter in proteomics, introducing a number of algorithms which enabled reliable, robust and quantitatively accurate large-scale experiments using high-throughput methods

flower

FlowER uses flow matching to model chemical reaction as a process of electron redistribution, conceptually aligns with arrow-pushing formalisms. It aims to capture the probabilistic nature of reactions with mass conservation where multiple outcomes are reached through branching mechanistic networks evolving in time.

ilastik

ilastik: the interactive learning and segmentation toolkit¶

keras

keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. It was developed with a focus on enabling fast experimentation. *Being able to go from idea to result with the least possible delay is key to doing good research.

molexa

molexa is a deep generative neural network capable of reconstructing molecular geometries from ion momentum measurements in X-ray-based Coulomb explosion imaging (CEI) experiments.

pocketxmol

pocketxmol is an AI generative model that learns fundamental atom interactions, enabling applications governed by atom interactions within a pocket, including, small-molecule docking, peptide docking, and molecular conformation generation, structure-based drug design (SBDD), fragment linking/growing, PROTAC design, de novo linear/cyclic peptide design, and peptide inverse folding.

pytorch

pytorch is a Python package that provides two high-level features: Tensor computation (like NumPy) with strong GPU acceleration, and Deep neural networks built on a tape-based autograd system

rapids

The rapids suite of open source software libraries and APIs gives you the ability to execute end-to-end data science and analytics pipelines entirely on GPUs.

rf2na

rf2na: RoseTTAFold2 protein/nucleic acid complex prediction

rosettafold

rosettafolds three-track network produces structure predictions with accuracy approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure.

scikit-image

scikit-image aims to be the reference library for scientific image analysis in Python.

scikit-learn

scikit-learn is a simple and efficient tools for data mining and data analysis

tensorflow

tensorflow™ is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them.