NAFlex – Analysis of Nucleic Acids Flexibility

NAFlex

:: DESCRIPTION

NAFlex is a web interface for the study of Nucleic Acids Flexibility.NAFlex allows the user to incorporate structures from the Protein Data Bank, filling gaps and removing structural inconsistencies if any. It also allows to build canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries and to create specific nucleic acids conformations.

::DEVELOPER

The Molecular Modeling and Bioinformatics (MMB) research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W47-55. doi: 10.1093/nar/gkt378. Epub 2013 May 17.
NAFlex: a web server for the study of nucleic acid flexibility.
Hospital A1, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M.

PredyFlexy – Flexibility and Local Structure prediction from sequence

PredyFlexy

:: DESCRIPTION

PredyFlexy is designed to predict local protein structures and protein flexibility from its sequence. Results can be visualised at the amino acid level through a table and graphics.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PredyFlexy

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W317-22. doi: 10.1093/nar/gks482. Epub 2012 Jun 11.
PredyFlexy: flexibility and local structure prediction from sequence.
de Brevern AG1, Bornot A, Craveur P, Etchebest C, Gelly JC.

tCONCOORD 1.0 – Predict Protein Conformational Flexibility

tCONCOORD 1.0

:: DESCRIPTION

tCONCOORD predicts protein conformational flexibility based on geometrical considerations. In a first step, the protein structure is analyzed and turned into a set of constraints, mostly distance constraints but also angle, chiral and planarity constraints with upper and lower bounds. This set of constraints serves as a kind of construction plan for the protein.

::DEVELOPER

Daniel Seeliger

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

tCONCOORD

:: MORE INFORMATION

Citation

Daniel Seeliger and Bert L. de Groot.
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.
J. Comp. Chem. 30:1160-1166 (2009)

PDBFlex – Exploring Flexibility in Protein Structures

PDBFlex

:: DESCRIPTION

The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric units of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2016 Jan 4;44(D1):D423-8. doi: 10.1093/nar/gkv1316. Epub 2015 Nov 28.
PDBFlex: exploring flexibility in protein structures.
Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A.