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ProDy — Protein Dynamics and Sequence Analysis

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. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.

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ProDy — Protein Dynamics and Sequence Analysis | prody.csb.pitt.edu Reviews

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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. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.

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7 prody

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ProDy — Protein Dynamics and Sequence Analysis | prody.csb.pitt.edu Reviews

https://prody.csb.pitt.edu

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. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.

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prody.csb.pitt.edu

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ProDy — Protein Dynamics and Sequence Analysis

http://prody.csb.pitt.edu/nmwiz

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. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.

2

PDB files — ProDy

http://prody.csb.pitt.edu/tutorials/structure_analysis/pdbfiles.html

Structure Analysis ». Show code snippets for copying:. Search terms or a module, class or function by name:. Series come with new and improved sequence, structure, and dynamics analysis features. See release notes. Bakan A, Meireles LM, Bahar I ProDy. Protein Dynamics Inferred from Theory and Experiments. This examples demonstrates how to use the flexible PDB fetcher,. Valid inputs are PDB identifier, e.g 2k39. Or a list of PDB identifiers, e.g. Compressed PDB files (. For failed downloads,. Parser can b...

3

NMR Models — ProDy

http://prody.csb.pitt.edu/tutorials/ensemble_analysis/nmr.html

Ensemble Analysis ». Compare with ANM results. Show code snippets for copying:. Search terms or a module, class or function by name:. Series come with new and improved sequence, structure, and dynamics analysis features. See release notes. Bakan A, Meireles LM, Bahar I ProDy. Protein Dynamics Inferred from Theory and Experiments. This example shows how to perform principal component analysis (PCA) of an ensemble of NMR models. The protein of interest is ubiquitin. And principal modes (. Principal modes c...

4

Heterogeneous X-ray Structures — ProDy

http://prody.csb.pitt.edu/tutorials/ensemble_analysis/xray.html

Ensemble Analysis ». Show code snippets for copying:. Search terms or a module, class or function by name:. Series come with new and improved sequence, structure, and dynamics analysis features. See release notes. Bakan A, Meireles LM, Bahar I ProDy. Protein Dynamics Inferred from Theory and Experiments. This example compares experimental structural data analyzed using Principal Component Analysis (PCA) with the theoretical data predicted by Anisotropic Network Model (ANM):. PCA - ANM overlap.

5

Atom Selections — ProDy

http://prody.csb.pitt.edu/manual/reference/atomic/select.html

ProDy Manual ». Reference Manual ». Atomic Data ». Show code snippets for copying:. Search terms or a module, class or function by name:. Series come with new and improved sequence, structure, and dynamics analysis features. See release notes. Bakan A, Meireles LM, Bahar I ProDy. Protein Dynamics Inferred from Theory and Experiments. This module defines a class for selecting subsets of atoms. You can read this page in interactive sessions using. ProDy offers a fast and powerful atom selection class,.

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MMBioS Software

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NIH Biomedical Technology and Research Resource (BTRR). Technology Research and Development. EAB Meeting Fall 2015. EAB Meeting Fall 2014. EAB Meeting Fall 2013. How to Acknowledge Us. The following software tools and services, developed by MMBioS partners, are freely available to the biomedical community. We ask that any publications resulting from their use include an acknowledgement. Elastic Network Models (ENM). CellBlender is a Blender addon for creation, simulation, visualization, and analysis of r...

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ProDy — Protein Dynamics and Sequence Analysis

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. Workflow for comparative analysis of sequence evolution and structural dynamics is shown. See Evol Applications. Or Mol Biol Evol article. Results from comparative analysis of residue conservation, conformational mobility, and coevolutionary patterns for uracil-DNA glycosylase. See Mol Biol Evol article. VMD plugin. See NMWiz tutorial.

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