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.
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.
Workflow for GNM analysis of chromatin dynamics. See publication for details.
Covariance matrix of chromosome 17 of human B cells. Structural domains and CCDDs are identified and outlined. See publication for details.
3D Laplacian embedding of chromosome 17 loci using the first three principal modes. See ChromD tutorial for details.
MechStiff calculates the mechanical resistance to external force (uniaxial tension) applied at specific pairs of residues on the 3D structure.
MechStiff uses as an input the known structure modeled as ANM. It may be used to evaluate the Mechanical Stiffness/Strength Map as a function of residue indices and effective stiffness (or force constant) for each residue averaged over all pairs it forms, plotted as 2D (map) or 1D (profile) respectively, along with the ribbon diagrams color-coded by residue strength (TCL script directly uploaded to VMD). The plots and vizualization can be used for:
ProDy is developed in Bahar Lab at the University of Pittsburgh. Click here to see a list of people who contributed to its development.
ProDy makes use of great open source software including NumPy, Pyparsing, Biopython, SciPy, and Matplotlib. Click here for details.
ProDy is open source and you can contribute to its development in many ways. See this guide for getting started.
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