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Use when working with ProteinShake, a Python library for protein 3D structure datasets and benchmark tasks that can be converted to graph, point-cloud, or voxel representations and loaded into PyTorch
Use with AI
Install the MCP server or CLI to instantly fetch ProteinShake documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/proteinshake
MDAnalysis — Python library for analyzing molecular dynamics trajectories and atomic coordinate data. Supports 40+ file formats (DCD, XTC, TRR, PDB, GRO, AMBER, LAMMPS). Provides RMSD, RMSF, hydrogen
3 shared topics • 2 shared operations
MDTraj — Python library for reading, writing, and analyzing molecular dynamics trajectories. Supports 20+ formats (DCD, XTC, TRR, PDB, HDF5, NetCDF, etc.) with NumPy-native arrays. Provides RMSD, RMSF
3 shared topics • 2 shared operations
Infernal — RNA covariance model (CM) toolkit for homology search and structural alignment of RNA sequences. Builds profile CMs from Stockholm alignments (cmbuild), calibrates E-values (cmcalibrate), s
3 shared topics • 1 shared operation
P2Rank — fast machine learning tool for predicting ligand binding sites from protein structure. Uses random forest classifier on physicochemical and geometric features of solvent-accessible surface po
3 shared topics • 1 shared operation
RoseTTAFold — deep learning-based protein structure prediction using a three-track neural network architecture for simultaneous processing of 1D sequence, 2D distance maps, and 3D coordinates. Predict
3 shared topics • 1 shared operation