Tag: Protein Flexibility

MPRDock – Protein-ensemble-RNA Docking by efficient Consideration of Protein Flexibility

MPRDock

:: DESCRIPTION

The MPRDOCK server is to predict the complex structure between proteins and nucleic acids through ensemble docking of multiple protein structures that are built based by homology modeling.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

He J, Tao H, Huang SY.
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.
Bioinformatics. 2019 Dec 1;35(23):4994-5002. doi: 10.1093/bioinformatics/btz388. PMID: 31086984.

FlexServ – Analysis of Protein Flexibility

FlexServ

:: DESCRIPTION

FlexServ is a project aimed to show in an easy and visual way flexibility-related properties of proteins.

::DEVELOPER

Molecular Modeling and Bioinformatics Unit , IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jul 1;25(13):1709-10. Epub 2009 May 7.
FlexServ: an integrated tool for the analysis of protein flexibility.
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D’Abramo M, Gelpí JL, Orozco M.

pFlexAna 0.1.1 – Protein Flexibility Analyzer

pFlexAna 0.1.1

:: DESCRIPTION

The pFlexAna  detects and displays conformational changes in remotely related proteins, without relying on sequence homology

::DEVELOPER

M2AP Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 pFlexAna

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W246-51. doi: 10.1093/nar/gkn259.
pFlexAna: detecting conformational changes in remotely related proteins.
Nigham A, Tucker-Kellogg L, Mihalek I, Verma C, Hsu D.

RCI – Prediction of Protein Flexibility using Random Coil Index

RCI

:: DESCRIPTION

RCI (Random Coil Index) webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W531-7. Epub 2007 May 7.
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts.
Berjanskii MV, Wishart DS.

RCI – Predict Protein Flexibility by Calculating Random Coil Index

RCI

:: DESCRIPTION

RCI (Random Coil Index) webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RCI

:: MORE INFORMATION

Citation

Mark V. Berjanskii, David S. Wishart (2005)
A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts.
Journal of the American Chemical Society, 127 (43), 14970 -14971