TITLE

A tool for calculating binding-site residues on proteins from PDB structures

PUB. DATE
January 2009
SOURCE
BMC Structural Biology;2009, Vol. 9, p52
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
No abstract available.
ACCESSION #
44172276

 

Related Articles

  • ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structure at different distance threshold. Firoz, Ahmad; Malik, Adeel; Afzal, Obaid; Jha, Vivekanand // Bioinformation;2010, Vol. 5 Issue 2, p55 

    To investigate the functional sites on a protein and the prediction of binding sites (residues) in proteins, it is often required to identify the binding site residues at different distance threshold from protein three dimensional (3D) structures. For the study of a particular protein chain and...

  • BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure. Porter, Craig T.; Martin, Andrew C. R. // Bioinformatics;12/15/2015, Vol. 31 Issue 24, p4017 

    We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib...

  • SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. Biro, Jan C.; Fördös, Gergely // BMC Bioinformatics;2005, Vol. 6, p170 

    Background: The interacting residues of protein and nucleic acid sequences are close to each other — they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to...

  • DECOMP: A PDB decomposition tool on the web. Ordog, Rafael; Szabadka, Zoltán; Grolmusz, Vince // Bioinformation;2009, Vol. 3 Issue 10, p413 

    The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB...

  • pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files. Lütteke, Thomas; Von Der Lieth, Claus-W. // BMC Bioinformatics;2004, Vol. 5, p69 

    Background: Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological...

  • CALCOM: A software for calculating the center of mass of proteins. Costantini, Susan; Paladino, Antonella; Facchiano, Angelo M. // Bioinformation;2008, Vol. 2 Issue 7, p271 

    The center of mass of a protein is an artificial point useful for detecting important and simple features of proteins structure, shape and association. CALCOM is a software which calculates the center of mass of a protein, starting from PDB protein structure files. In the case of protein...

  • A series of PDB-related databanks for everyday needs. Touw, Wouter G.; Baakman, Coos; Black, Jon; te Beek, Tim A. H.; Krieger, E.; Joosten, Robbie P.; Vriend, Gert // Nucleic Acids Research;Jan2015, Vol. 43 Issue D1, pD364 

    We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry...

  • PDBToSDF: Create ligand structure files from PDB file. Muppalaneni, Naresh Babu; Rao, Allam Appa // Bioinformation;2011, Vol. 6 Issue 10, p383 

    Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the...

  • Pre-calculated protein structure alignments at the RCSB PDB website. Prlić, Andreas; Bliven, Spencer; Rose, Peter W.; Bluhm, Wolfgang F.; Bizon, Chris; Godzik, Adam; Bourne, Philip E. // Bioinformatics;Dec2010, Vol. 26 Issue 23, p2983 

    Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure...

  • PDB explorer - A web based algorithm for protein annotation viewer and 3D visualization. Nayarisseri, Anuraj; Shardiwal, Rakesh; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza // Interdisciplinary Sciences: Computational Life Sciences;Dec2014, Vol. 6 Issue 4, p279 

    The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics