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Personalization of structural PDB files

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Woźniak T., Adamiak R.

2013

vol. 60

issue 4

591-593

PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions. PDBinout is freely available under the LGPL licence at http://pdbinout.ibch.poznan.pl

Identification of antimicrobial peptides by using eigenvectors

100%

Polanco C.

2016

vol. 63

issue 3

483-491

Antibacterial peptides are subject to broad research due to their potential application and the benefit they can provide for a wide range of diseases. In this work, a mathematical-computational method, called the Polarity Vector Method, is introduced that has a high discriminative level (>70%) to identify peptides associated with Gram (-) bacteria, Gram (+) bacteria, cancer cells, fungi, insects, mammalian cells, parasites, and viruses, taken from the Antimicrobial Peptides Database. This supervised method uses only eigenvectors from the incident polar matrix of the group studied. It was verified with a comparative study with another extensively verified method developed previously by our team, the Polarity Index Method. The number of positive hits of both methods was up to 98% in all the tests conducted.

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2 Acta Biochimica Polonica

1 2016

1 2013

1 Adamiak R.

1 Polanco C.

1 Woźniak T.

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Personalization of structural PDB files

Identification of antimicrobial peptides by using eigenvectors