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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
  1. aRead and search functionality.
  2. bRead-only functionality from the PDB.
  3. cRead, search, and annotation functionality, including enhanced search capabilities across multiple databases.
  4. dSTM: Spring Tensor Model; pANM: power ANM; nnANM: nearest neighbor ANM; mcgANM: mixed coarse graining ANM.
  5. eDependences are not open source.
  6. fVMD plugin NMWiz available for single molecule NMA.
  7. gWeb interface for ensemble PCA and NMA in development.