AlphaFold2

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 • 2 shared operations

ColabFold — fast protein structure prediction combining AlphaFold2 with MMseqs2 for rapid MSA generation. Predict monomer and multimer structures, generate multiple sequence alignments, run batch pred

2 shared topics • 3 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

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 • 1 shared operation

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 • 1 shared operation