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T-DB specifications


Unique identifier OMICS_03656
Name T-DB
Alternative name TOPOFIT-DB
Restrictions to use None
Maintained No

Publication for TOPOFIT-DB

T-DB citations


Fractional Transport of Photons in Deterministic Aperiodic Structures

Sci Rep
PMCID: 5442164
PMID: 28536441
DOI: 10.1038/s41598-017-02170-9

[…] ted-order, . The distributed-order time fractional diffusion equation can be obtained from the FDWE by integrating with respect to the order β the fractional time derivative as follows:5∫01p(β)D⁎βφ(x,t)dβ=D∂xxφ(x,t)where p(β) is a non-negative dimensionless weight function subject to the normalization condition ∫01p(β)dβ=1. Clearly when the weight is a delta function the distributed-order time fra […]


Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii) in China from Mitochondrial Control Region and Nuclear Intron Sequences

Int J Mol Sci
PMCID: 4519862
PMID: 26132567
DOI: 10.3390/ijms160714623

[…] Prior distributions were defined for three sets of analyses as follows: 1 < t1 < t2 < t3 < t4 < 100; 5 < db < 25; 1000 < N < 1,000,000; 1 < Nf < 10,000. The values of the demographic parameters were t, db, N and Nf. The values of the sample sizes that were measured in number of individuals were N and Nf. The values of times that were measured in number of generations were db and t. The default va […]


A comprehensive analysis of non sequential alignments between all protein structures

BMC Struct Biol
PMCID: 2213659
PMID: 18005453
DOI: 10.1186/1472-6807-7-78

[…] ary structure element definition. The method is also computationally efficient, so that all proteins in the PDB (as of July 2005) have already been calculated, grouped into clusters and stored in the TOPOFIT-DB database []. We have used TOPOFIT in our comprehensive large-scale analysis of non-sequential relations between proteins. To the best of our knowledge this is the first comprehensive large- […]


Changing Cellular Location of CheZ Predicted by Molecular Simulations

PLoS Comput Biol
PMCID: 1447658
PMID: 16683020
DOI: 10.1371/journal.pcbi.0020039

[…] random directions by distances calculated from Fick's second law rewritten as a stochastic master equation: , with pB(r,t), spatial probability density of a single B molecule at position r and time t; DB, diffusion coefficient for a B molecule. The product pB(r,t)dr is the probability that a specific B molecule is within a volume dr about position r at time t. Solving the above equation shows th […]


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T-DB institution(s)
Department of Biology, Northeastern University, Boston, MA, USA

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