BetaProbe: A probability based method for predicting beta sheet topology using integer programming

Eghdami, Mahdie; Dehghani, Toktam; Naghibzadeh, Mahmoud

doi:10.1109/iccke.2015.7365819

Cited by 6 publications

(2 citation statements)

References 26 publications

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“…Precision Recall Betapro [15] 0.59 0.54 BCov [30] 0.60 0.62 BetaProbe [18] 0.67 0.70 Top-DBS [17] 0.75 0.78 Current Study 0.67 0.57 One of the reasons why the results from our study could not match those from more recent studies may be that the topology filter, in its current form, is too coarse. Suppose we have a protein with three β-strands.…”

Section: Programmentioning

confidence: 66%

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Topology of protein metastructure and $β$-sheet topology

Andersen¹,

Fuji²,

Koyanagi³

2021

Preprint

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We introduce a new, simplified model of proteins, which we call protein metastructure. The metastructure of a protein carries information about its secondary structure and β-strand conformations. Furthermore, protein metastructure allows us to associate an object called a fatgraph to a protein, and a fatgraph in turn gives rise to a topological surface. It becomes thus possible to study the topological invariants associated to a protein. We discuss the correspondence between protein metastructures and fatgraphs, and how one can compute topological invariants, such as genus and the number of boundary components, from fatgraphs. We then describe an algorithm for generating likely candidate metastructures using the information obtained from topology of protein fatgraphs. This algorithm is further developed to predict β-sheet topology of proteins, with a possibility to combine it with an existing algorithm. We demonstrate the algorithm on the data from PDB, and improve the performance of and existing algorithm by combining with it.

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Section: Programmentioning

confidence: 66%

“…One may also combine the two methods by, for example, forbidding certain β-strand configurations that are not found in the database [32], or by incorporating the two in Bayesian modelling [12]. Other studies used integer programming techniques to predict β-sheet topologies [30,18].…”

Section: Introductionmentioning

confidence: 99%