TM-score 20190822 – Calculate Similarity of Topologies of two Protein Structures

TM-score 20190822

:: DESCRIPTION

TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TM-score

:: MORE INFORMATION

Citation

J. Xu, Y. Zhang,
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics, 2010 26, 889-895

rSPR 1.3.0 – Calculate Rooted Subtree-prune-and-regraft Distances and rooted agreement forest

rSPR 1.3.0

:: DESCRIPTION

rSPR (rooted subtree-prune-and-regraft) is a software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Perl
  • C++ Compiler

:: DOWNLOAD

  rSPR

:: MORE INFORMATION

Citation

Whidden, C., Beiko, R.G., Zeh, N.
Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments.
In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010)

SPRSupertrees 1.2.1 – Calculate Rooted Supertrees that Minimize the SPR Distance.

SPRSupertrees 1.2.1

:: DESCRIPTION

SPR Supertrees is a software package for computing supertrees that minimize the SPR distance.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • C++ Compiler

:: DOWNLOAD

 SPRSupertrees

:: MORE INFORMATION

Citation

Whidden, C., Zeh, N., Beiko, R.G. (2013)
Supertrees based on the subtree prune-and-regraft distance.
PeerJ PrePrints 1:e18v1

MAXPROC – Calculate Maximum Likelihood Estimates of Linkage Parameters

MAXPROC

:: DESCRIPTION

MAXPROC calculates maximum likelihood estimates of linkage parameters under heterogeneity and their standard errors using EM and SEM algorithms

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MAXPROC

:: MORE INFORMATION

Citation

Biswas S and Lin S (2003).
Evaluation of maximization procedures for estimating linkage parameters under heterogeneity.
Genetic Epidemiology, 26, 206-217.

MSTgold 2.5 – Calculates Minimum Spanning Trees

MSTgold 2.5

:: DESCRIPTION

MSTgold calculates minimum spanning trees (MST) from protein and nucleotide sequences, from binary characters and SNPs, and from tab-delimited data such as microsatellite data. It also estimates the number of different MSTs from a data set, bootstraps MSTs, and identifies the most reliable tree among a set of equal-length MSTs.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 MSTgold

:: MORE INFORMATION

Citation

Stephen J. Salipante and Barry G. Hall
Inadequacies of Minimum Spanning Trees in Molecular Epidemiology
J. Clin. Microbiol. October 2011 vol. 49 no. 10 3568-3575

GrowthRates 4.0 – Calculates Bacterial Growth Rates

GrowthRates 4.0

:: DESCRIPTION

GrowthRates is a program that calculates bacterial growth rates from the data generated by a micro-plate reader used to monitor the growth of bacterial cultures in micro-plate wells. The program automatically identifies the exponential phase of the growth curve and uses that portion of the curve to calculate growth rates and std. errors of those rates

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GrowthRates

:: MORE INFORMATION

Citation

Statistical Package for Growth Rates Made Easy.
Mira P, Barlow M, Meza JC, Hall BG.
Mol Biol Evol. 2017 Dec 1;34(12):3303-3309. doi: 10.1093/molbev/msx255.

AVP 1.3 – Calculate Protein Void Volumes and Packing Quality

AVP 1.3

:: DESCRIPTION

AVP (Another Void Program) is a new method for the analysis of voids in proteins and packing quality in a single united program. Traditionally been analysed using different approaches, but in reality they are extremes of the same phenomenon – imperfect packing of atoms in the inside of a protein.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AVP

:: MORE INFORMATION

Torsions – Calculates Backbone Torsion Angles from a PDB file

Torsions

:: DESCRIPTION

TORSIONS is a simple program to read a PDB file and calculate backbone torsion angles. It calculates phi, psi and omega and can also calculate C-alpha pseudo-torsions.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Torsions

:: MORE INFORMATION

K-Estimator 6.1v – Calculate the number of Nucleotide Substitutions

K-Estimator 6.1v

:: DESCRIPTION

K-Estimator is a software that estimates the number of of synonymous (Ks) and nonsynonymous substitutions (Ka) per site (divergence) when comparing two aligned nucleotide sequences, both protein-coding and non-coding. Confidence intervals of the divergence estimates are obtained by Monte Carlo simulation.

::DEVELOPER

Josep M. Comeron

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

K-Estimator

:: MORE INFORMATION

Citation

Comeron JM. (1999)
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals.
Bioinformatics 15(9):763-764.

Molar Mass Calculator 1.1.1 – Calculate Chemical Formula Molar Mass

Molar Mass Calculator 1.1.1

:: DESCRIPTION

Molar Mass Calculator calculats chemical formula molar mass  by adding up the individual molar masses of its constituent elements. Given a chemical formula this iPad app will calculate molar mass and subtotal masses for the substance.

::DEVELOPER

Thundercloud Consulting, LLC

:: SCREENSHOTS

MolarMass

:: REQUIREMENTS

  • iOS

:: DOWNLOAD

 Molar Mass Calculator

:: MORE INFORMATION