Tag: Determine

SnB 2.3 – Determine Crystal Structures from X-ray Diffraction Data

SnB 2.3

:: DESCRIPTION

SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone. Recently, SnB has also been used to determine the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites.

::DEVELOPER

SnB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SnB

:: MORE INFORMATION

Citation:

SnB version 2.3: triplet sieve phasing for centrosymmetric structures.
Xu H, Smith AB, Sahinidis NV, Weeks CM.
J Appl Crystallogr. 2008;41:644-646.

EnzymeX 3.3.3 – Determine Restriction Enzymes

EnzymeX 3.3.3

:: DESCRIPTION

EnzymeX helps molecular biologists determine which restriction enzymes they should use to cut their DNA of interest, along with complete DNA sequence analysis and editing.

::DEVELOPER

Nucleobytes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Mac OsX

:: DOWNLOAD

EnzymeX

:: MORE INFORMATION

MAPPS 1.1.6 – Determine Nucleotide Model Adequacy

MAPPS 1.1.6

:: DESCRIPTION

MAPPS is a program for determining nucleotide model adequacy.

::DEVELOPER

Jonathan P Bollback

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 MAPPS

:: MORE INFORMATION

Citation

Bollback, J.P. (2002)
Bayesian Model Adequacy and Choice in Phylogenetics.
Molecular Biology and Evolution. 19(7): 1171-1180.

PCPMer 3.5.6 – Determine Conserved Regions in multiple Sequence Alignments

PCPMer 3.5.6

:: DESCRIPTION

PCPMer (Physical Chemical Property Based Motif Analyzer ) is a software package for determining conserved regions in multiple sequence alignments. The software represents each of the 20 naturally occuring amino acids by five quantitative descriptors and can detect motifs (short regions of significant conservation) in aligned sequences based on relative entropy or physicochemical similarity. It can be then used to search for related proteins in a protein sequence database and map the variability data on a 3D structure (to make a stereophysicochemical variability plot, or SVP). Such plots are particularly useful for identifying the spatial relationships of highly conserved or variable residues to one another.

::DEVELOPER

 PCPMer Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PCPMer

:: MORE INFORMATION

Citation:

Schein, C.H., Zhou, B. and Braun, W.
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
Virol. J. Apr 21;2(1):40, 2005

 

WHICHPARENTS 1.0 – Use Mutlilocus Genotype data to Determine the Most likely Parents of Offspring

WHICHPARENTS 1.0

:: DESCRIPTION

WHICHPARENTS is an application for determining the most likely parents of offspring, using mutlilocus genotype data. If parental mating history is known, this program also makes use of that information.

::DEVELOPER

Dennis Hedgecock, @ BODEGA MARINE LABORATORY

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 WHICHPARENTS

:: MORE INFORMATION

DomainFinder 2.0.4 – Determine Dynamical Domains in Protein

DomainFinder 2.0.4

:: DESCRIPTION

DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are

  1. computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes
  2. ease of use: a state-of-the-art graphical user interface
  3. export of results for visualization and further analysis (VRML, PDB, and MMTK object format)

::DEVELOPER

Konrad Hinsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DomainFinder

:: MORE INFORMATION

Citation:

K. Hinsen
Analysis of domain motions by approximate normal mode calculations
Proteins 33(3), 417-429 (1998)