NAMD

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

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

Open Babel — open-source cheminformatics toolkit for chemical file format conversion, 3D coordinate generation, molecular fingerprint calculation, substructure and SMARTS pattern searching, descriptor

3 shared topics

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

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