SULDEX 0.01 – Simultaneous Ultra high throughput Ligand Dissociation EXperiment

SULDEX 0.01

:: DESCRIPTION

The SULDEX packages is designed to use high throughput sequencing to simultaneously analyze binding dissociation constants for large repertoires of sequences.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler

:: DOWNLOAD

SULDEX

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e26105. doi: 10.1371/journal.pone.0026105. Epub 2011 Nov 1.
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.
Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ.

CooperativeDimer – Analysis of Ligand Binding to Dimers

CooperativeDimer

:: DESCRIPTION

CooperativeDimer is a software developed in Mathematica for the analysis of the affinities and any cooperativity in ligand binding to a dimer (or other molecule containing two equivalent binding sites). The approach requires data on the fractional populations of all three species (apo, singly and doubly bound) such as may be obtained from mass spectrometry or NMR data.

::DEVELOPER

Mark A. Williams

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Mathematica

:: DOWNLOAD

CooperativeDimer

:: MORE INFORMATION

Citation

Marcus J. Edwards, Mark A. Williams, Anthony Maxwell and Adam R. McKay (2011).
Mass spectrometry reveals the antibiotic simocyclinone D8 binds DNA gyrase in “bent over” conformation: evidence for positive coperativity.
Biochemistry. 2011 May 3;50(17):3432-40. Epub 2011 Apr 5.

LigAlign 1.0 – Ligand-based Active site Alignment and Analysis

LigAlign 1.0

:: DESCRIPTION

LigAlign is a free plugin for PyMOL which implements a novel algorithm for ligand-fragment-based active site alignment. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.

::DEVELOPER

Lilien Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python
PyMOL

:: DOWNLOAD

LigAlign

:: MORE INFORMATION

Citation

Heifets, A., Lilien, R.,
LigAlign: Flexible ligand-based active site alignment and analysis.
Journal of Molecular Graphics and Modelling. Volume 29, Issue 1, 24 August 2010, Pages 93-101.

CCOMP 3.70 – Compare Ligand/Receptor Complexes

CCOMP 3.70

:: DESCRIPTION

CCOMP (Complex COMParison) is a simple command-line tool for comparing ligand/receptor complexes. It can also be used for calculating pairwise all-atom RMSD of slightly different protein structures, taking care of missing atoms, sequence inconsistencies, etc. CCOMP reads two files in PDB format, including both a receptor and a ligand, computes a pairwise sequence alignment of the receptor molecules, generates alpha-carbon superposition of the receptor structures according to the generated alignment, and computes individual deviations per residuum.

::DEVELOPER

Piotr Rotkiewicz

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows

:: DOWNLOAD

CCOMP

:: MORE INFORMATION

Citation

W. Sicinska, P. Rotkiewicz,
“Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptor,”
J. Ster. Biochem. Mol. Biol., 103 (3-5), 305-309 (2007)