Official git repository for Biopython (originally converted from CVS)
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Updated
May 13, 2024 - Python
Official git repository for Biopython (originally converted from CVS)
Base Scipion plugin defining objects and protocols for CHEMoinformatics
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Saprot: Protein Language Model with Structural Alphabet
A collection of research papers for AI-based protein design
Structure-aware adapter fine-tuning PLMs, with high training speed and impressive performance.
Fusion of protein sequence and structural information, using denoising pre-training network for protein engineering (zero-shot).
macromolecular crystallography library and utilities
The Integrative Modeling Platform
mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
C++ package that provides tools for correcting structural predictions of proteins (eg. from X-Ray Crystallography or AlphaFold) using X-ray small-angle scattering (SAXS) in solution
A NumPy port of the foldseek code for encoding protein structures to 3di.
Extraction of correlations from multistate PDB protein coordinates
The Rosetta Bio-macromolecule modeling package.
Foldseek enables fast and sensitive comparisons of large structure sets.
Modeling molecular ensembles with scalable data structures and parallel computing
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
Calculation of interatomic interactions in molecular structures
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