Dynamics of p38 MAP kinase inferred from a structural ensemble using PCA is compared to intrinsic dynamics of the protein modeled using ANM. See PCA of X-ray structures or Bioinformatics article for more details.

Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications or Mol Biol Evol article for more details.

Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article or Conservation and Coevolution Analysis for more details.

Coevolution of NEF-binding residues analzyed using mutual information is displayed for the Hsp70 ATPase domain. See PLoS Comp Biol article or Conservation and Coevolution Analysis for details.

Comparative analysis of p38 MAP kinase dynamics from experiments (PCA) and theory (ANM). See the PNAS article or figure for details.

Comparative analysis of dynamics of drug target proteins and model systems from experiments (PCA) and theory (ANM). See the Protein Science article for details.

Comparative analysis of p38 MAP kinase dynamics from experiments (PCA), simulations (EDA), and theory (ANM). See the Protein Science article for details.

Animation shows HIV-1 reverse transcriptase functional motions calculated using anisotropic network model. Arrows and animations are generated using NMWiz VMD plugin. See NMWiz tutorial for usage examples.

You can make a quick protein representation in interactive sessions using showProtein() function.

NMWiz is designed for picturing normal modes easy. Image shows arrows from slowest three ANM modes for p38 MAP kinase centered at the origin. They indeed align with planes normal to each other.

NMWiz makes depicting elastic network models and protein motions predicted with them easy. Image shows ANM model for p38 MAP kinase and three slow ANM modes (below).

NMWiz can be used to comparative dynamics inferred from experimental datasets and predicted using theory.

• 

  ProDy Project

  ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development.

  Evol for Bridging Evolution and Dynamics

  Evol is a suite of new applications and modules built in ProDy for analysis of sequence evolution and characterization of dynamical properties of conserved and coevolved amino acid residues. See Sequence Evolution for more details.

  Normal Mode Wizard (NMWiz)

  NMWiz is a VMD plugin and a GUI. NMWiz can be used to execute ProDy applications and perform comparative visual analysis of protein dynamics and coevolution. See NMWiz section for details.

  Download

  ProDy has been downloaded more than 100,000 times since Nov 2010 and is used at over 120 academic institutions worldwide. Latest release is v1.4.2. See Getting ProDy for downloads and installation instructions or Changes to see what's new.

  How to Use

  You may start from the Tutorial, one of the detailed usage Examples. or browse the contents of the Documentation.

  Reference

  ProDy: Protein Dynamics Inferred from Theory and Experiments Bakan A, Meireles LM, Bahar I 2011 Bioinformatics 27(11):1575-1577

• 

  ProDy for Protein Dynamics Analysis

  ProDy allows for efficient analysis of large structural datasets and modeling of protein structural dynamics. Following are some detailed examples of what you can do:

  Dynamics analysis

  • Principal component analysis can be performed for
    • heterogeneous X-ray structures (missing residues, mutations)
    • mixed structural datasets from Blast search
    • NMR models and MD snapshots (essential dynamics analysis)
  • Normal mode analysis can be performed using
    • Anisotropic network model (ANM)
    • Gaussian network model (GNM)
    • ANM/GNM with Distance and property dependent force constants

  Dynamics inferred from experimental datasets can be compared to theoretical models and computational datasets conveniently. See comparative analysis and visualization examples.

  Structural analysis

  ProDy can also be used for structural analysis. It has fast and flexible parsers for PDB files and DCD trajectories. Powerful and customizable atom selections allow for contact identification and matching, superposing, and comparing multiple structures/chains.

  Publications using ProDy

  • Bakan A, Bahar I 2009 PNAS 106(34):14349-14354 on intrinsic dynamics and ligand binding.
  • Bakan A, Bahar I 2011 Pac Symp Biocomput 16:181-192 on computational generation of inhibitor-bound protein conformers.
  • Meireles L, Gur M, Bakan A, Bahar I 2011 Protein Science 10(20):1645-1658 a review on intrinsic dynamics and ligand binding.

• 

  Evol for Bridging Evolution and Dynamics

  Evol is a set of new powerful and efficient API features and applications for analysis of sequence evolution and its comparison to protein functional dynamics.

  API Features

  • functions for searching Pfam and retrieving MSA files
  • extremely fast MSA IO functions
  • flexible MSA class with sequence indexing
  • functions for fast calculation and plotting of Shannon entropy and mutual information

  Applications

  Evol applications allow you to analyze large MSA files, save or plot numerical results without writing any code. You can read the output files and resume analysis in your favorite software.

  Download

  Evol is distributed with ProDy package. See Getting ProDy for downloads and installation instructions or Changes to see what's new.

  How to Use

  See Evol applications page or one of the sequence analysis examples.

  Publications

  • Sequence Evolution Correlates with Structural Dynamics Liu Y, Bahar I 2012 Mol Biol Evol 29(9):2253-2263
  • Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs Liu Y, Gierasch LM, Bahar 2010 PLoS Comput Biol 6(9)

• 

  Normal Mode Wizard

  Normal Mode Wizard (NMWiz) is a VMD plugin designed for visual comparative analysis of normal mode data, i.e. modes may come from principal component, essential dynamics, normal mode analysis or may be any vector describing a molecular motion.

  NMWiz allows you to:

  • perform ANM, GNM, and PCA/EDA calculations
  • draw customizable normal mode arrows
  • make animations (sample conformations)
  • make interactive square-fluctuations plots
  • compare two structures and draw deformation arrows

  Download

  NMWiz is distributed with VMD since v1.9.1. For updates that are not yet available in VMD latest release, check out Getting NMWiz.

  How to Use

  Usage examples can be found in NMWiz Tutorial and NMWiz documentation. You can input normal mode data to NMWiz in NMD Format or any other format recognized by VMD.

  Reference

  ProDy: Protein Dynamics Inferred from Theory and Experiments Bakan A, Meireles LM, Bahar I 2011 Bioinformatics 27(11):1575-1577

• Acknowledgments

  People

  ProDy project is initiated, designed, and developed by Ahmet Bakan in Bahar lab at the University of Pittsburgh.

  Evol applications and modules were co-developed with Anindita Dutta.

  See the full list of contributors to the ProDy project in People page.

  Community

  ProDy makes use of the following great software developed by the open source community:

  • Pyparsing for the sophisticated atom selection grammar.
  • Biopython KDTree package and pairwise2 module.
  • Numpy for speed and flexibility in almost all major functionality.
  • Finally, ProDy can benefit from Scipy and Matplotlib packages.

  Funding

  Support from NIH grants 1R01GM099738-01 for development and maintenance of ProDy is gratefully acknowledged. See more grant information in Funding page.

• Documentation

  You can browse a detailed list of contents or jump to a section from here.

  Tutorial overview of basic tasks Applications command line applications

  Examples detailed usage examples NMWiz NMWiz VMD plugin

  Reference API documentation Changes history of changes

  Documentation is also available in a single PDF file for offline reading.

  Literature

  Publications list of relevant publications

  Bibliography list of cited articles

  Reports development/performance notes

  Acknowledgments

  People developers and contributors

  Credits required/incorporated software

  Funding funding and support

  Index and Search

  Module Index list of all modules

  General Index all functions, classes, terms

  Search page search the documentation