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.

SuperMimic – Fit Peptide Mimetics into Protein Structures

SuperMimic

:: DESCRIPTION

SuperMimic is a tool for conformer based fitting of peptide mimetics into protein structures.Many protein recognition mechanisms, mostly involving other proteins or peptides, are known, and more and more of them are being deciphered. To intervent these interactions is the main goal of drug design. As peptides are often poor drug candidates, the need for bioequivalent compounds with better pharmacological properties arises. Starting from a known spatial structure, the goal is to find compounds that mimic the function of a peptide while obtaining improved cellular transport properties, stable structures and resistance against proteases.

The approach used in the program SuperMimic is to identify peptide mimetics starting from a known protein structure and conformations of a mimic, which are spatially superposed with the protein backbone. A compound library with peptidomimetic compounds collected from the literature as well as several protein structure libraries are provided, which can be scanned exhaustively.

::DEVELOPER

Andrean Goede

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SuperMimic

:: MORE INFORMATION

Citation:

SuperMimic – Fitting peptide mimetics into protein structures
Reviewed by Andrean Goede, Elke Michalsky, Ulrike Schmidt, and Robert Preissner
BMC Bioinformatics. 2006; 7: 11.