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.

The movie shows a molecular dynamics simulation for assessing the druggability of kinesin eg5. NMWiz VMD plugin. See NMWiz tutorial for usage examples.

Kinesin Eg5 druggable sites, including allosteric inhibitor binding site and and tubulin binding site, identified by simulations are shown. See our publication for details.

Sampling of the functional substates (inward-facing (IF) or outward-facing (OF), in closed (c) or open (o) forms) of LeuT using coMD simulations. See publication for details.

The movie illustrates a coMD trajectory for adenylate kinase. NMWiz VMD plugin. See NMWiz tutorial for usage examples.

Energy landscape in the space of principal coordinates.

Outward-facing (OF) and inward-facing (IF) structures of GltPh show a large displacement of the core domains. See publication for details.

The second mode of the OF structure moves all three transport domains simultaneously through the membrane in a ‘lift-like’ motion. See publication for details.

The second mode of the IF structure moves all three transport domains simultaneously through the membrane in a ‘lift-like’ motion. See publication for details.

Deformability profile of ubiquitin (PDB code: 1UBI). Structure is automatically uploaded to VMD program where blue color shows regions which are mechanically more resistant to the external force.

Mean value of effective spring constant (calculated from mechanical stiffness matrix) with secondary structure of ubiquitin. Blue color indicates mechanically strong regions.

Mechanical Stiffness Map with effective force constant in a color bar (blue - strong regions, red - weak regions) for ubiquitin.

Evol for Coevolution Analysis

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

API Features

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.

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)

People

ProDy is developed in Bahar Lab at the University of Pittsburgh. Click here to see a list of people contributed to its development.

Community

ProDy makes use of great open source software including NumPy, Pyparsing, Biopython, SciPy, and Matplotlib. Click here for details.

Source Code

ProDy is open source and you can contribute to its development in many ways. See this guide for getting started.

Problems?

Let us know any problems you might have by opening an issue at the tracker so that we can make ProDy better.