Table 1 Related software for analysis of protein structural dynamics
From: Integrating protein structural dynamics and evolutionary analysis with Bio3D
MMTK 2.7 | ProDy 1.5 | MAVEN 1.2 | WebNM@ 2.0 | Bio3D 2.0 | |
|---|---|---|---|---|---|
Dependencies | Python, NumPy, ScientificPython | Python, NumPy, MatplotLib | Matlab Component Runtime (MCR) | Web browser | R, Muscle |
Reading and analysis of molecular sequences | No | Yes | No | No | Yes |
Reading and analysis of multiple molecular structures | No | Yes | Yes | Yes | Yes |
Reading and analysis of binary MD simulation trajectories | Yes | Yes | No | No | Yes |
Biomolecular database integration | No | PDB, PFAMa | Nob | Nob | PDB, PFAM, UNIPROT, NRc |
Energy minimization and MD | Yes | No | No | No | No |
Standard NMA | Yes | Yes | Yes | Yes | Yes |
Ensemble NMA across heterogeneous structures | No | No | No | Yes | Yes |
Forcefields for NMA | C-alpha, ANM, Amber all-atom | GNM/ANM, Custom | GNM/ANM, pANM, STM, nnANM, mcgANM, Customd | C-alpha | C-alpha, ANM, pfANM sdENM, REACH, Custom |
Ensemble PCA across heterogeneous structures | No | Yes | Identical structures only | No | Yes |
Correlation network analysis from NMA and MD | No | No | No | No | Yes |
Dynamic domain analysis | No | No | No | No | Yes |
Sequence alignment | No | No | No | No | Yes |
Structure alignment | Yes | Yes | No | No | Yes |
Advanced statistical analysis | No | No | No | No | Yes |
Permits both interactive and batch analysis | Yes | Yes | No | Yes | Yes |
Open source code available | Yes | Yes | Yese | No | Yes |
Multicore compatibility | Yes | No | No | No | Yes |
GUI | No | Nof | Yes | Webserver | Nog |