NQ-Flipper 2.7 – Validate Asparagine and Glutamine Side-chain Amide Rotamers in Protein Structures

NQ-Flipper 2.7

:: DESCRIPTION

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures. This service is applicable to structures obtained from X-ray crystallography, NMR or modeling studies. The method is based on knowledge-based potentials of mean force compiled from a database of known protein structures determined by X-ray crystallography. The potentials are then refined by several cycles of rotamer correction and recompilation of potentials. The refined potentials are used here to validate or correct asparagine and glutamine amide rotamers.

::DEVELOPER

C.A.M.E. – the Center of Applied Molecular Engineering.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  NQ-Flipper

:: MORE INFORMATION

Citation

Weichenberger, C. X., and Sippl, M. J. (2006)
NQ-Flipper: Validation and Correction of Asparagine/Glutamine Amide Rotamers in Protein Crystal Structures.
Bioinformatics, 22, 1397-1398.

ProSa 2003 – Protein Structure Research Tool

ProSa 2003

:: DESCRIPTION

ProSa is a powerful tool in protein structure research. ProSa supports and guides your studies aimed at the determination of a protein’s native fold. It is helpful for experimental structure determinations and modeling studies.

ProSa Online Version

::DEVELOPER

C.A.M.E. – the Center of Applied Molecular Engineering.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 ProSa

:: MORE INFORMATION

Citation

Manfred Sippl(1993),
Recognition of Errors in Three-Dimensional Structures of Proteins,
Proteins 17, 355-362.

Wiederstein & Sippl (2007)
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
Nucleic Acids Research 35, W407-W410.

QuickPDB 20021101 – Java Applet for quickly viewing PROTEIN PDB Structure

QuickPDB 20021101

:: DESCRIPTION

QuickPDB permits you to find and quickly review a macromolecular structure looking at interactions between sequence and structure. Typically, once you have located structure(s) of interest you would download then for further analysis using local programs. QuickPDB is also available from the View Structure section of the Structure Explorer page for any entry in the Protein Data Bank .

::DEVELOPER

the Bourne Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX.
  • Java

:: DOWNLOAD

  QuickPDB

:: MORE INFORMATION

RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

NOC 3.01 – Molecular Explorer for Protein Structure Visualization

NOC 3.01

:: DESCRIPTION

NOC (also known as NOCH)  is a free molecular explorer for protein structure visualization, validation and analysis. It allows for import of molecular structures described in the Protein Data Bank file format.

::DEVELOPER

M.E. Chen, H.X. Cang, H. Nymeyer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

NOC

:: MORE INFORMATION

N/A

Voronoia 1.0 – Analyse Packing of Protein Structures

Voronoia 1.0

:: DESCRIPTION

Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.

::DEVELOPER

Charité Berlin – Structural Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Voronoia

:: MORE INFORMATION

Citation

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.
Voronoia: analyzing packing in protein structures.
Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5.

TASSER-Lite 1.0 – Protein Structure Modeling tool

TASSER-Lite 1.0

:: DESCRIPTION

TASSER-Lite is a protein structure comparative modeling tool. It is limited to protein target-template pairs whose pairwise sequence identity is >25% to the best threading template. It is optimized to model single domain proteins whose lengths range from 41-200 residues.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TASSER-Lite

:: MORE INFORMATION

Citation

Pandit, S B, Zhang Y, Skolnick J. 2006.
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal. 91(11):4180-90.