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PSAIA specifications

Information


Unique identifier OMICS_15453
Name PSAIA
Alternative name Protein Structure and Interaction Analyzer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A protein data bank structure.
Input format TXT
Output format TXT and XML
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License Academic Free License version 3.0
Computer skills Medium
Stability Beta
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kristian Vlahovicek

Publication for Protein Structure and Interaction Analyzer

PSAIA citations

 (16)
library_books

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism

2017
Sci Rep
PMCID: 5335569
PMID: 28256632
DOI: 10.1038/srep43885

[…] re, which is especially notable since the Trp31 and Trp70 residues lie at the entrance of the catalytic site of CB ().Analysis of the CA/CB interface at the crystallographic and SAXS models using the PSAIA software shows that the physical-chemical nature of the residues in the CA/CB interface are similar in both models (). This analysis shows that γ-chain does not make any contacts with CB in eith […]

library_books

Incorporation of protein binding effects into likelihood ratio test for exome sequencing data

2016
BMC Proc
PMCID: 5133515
PMID: 27980649
DOI: 10.1186/s12919-016-0043-8

[…] th index (DPX), (6) statistics on protrusion, and (7) length of the sequence. The secondary structure is from DSSP (dictionary of protein secondary structure) [] and other features are extracted from PSAIA (protein structure and interaction analyzer) []. As in the case of sequence-based classifiers, we apply a heterodimer structure-based binding site classifier with the highest f-measure obtained […]

library_books

GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N linked and O linked glycoproteomes by incorporating structural features

2016
Sci Rep
PMCID: 5052564
PMID: 27708373
DOI: 10.1038/srep34595

[…] d psi represent two types of International Union of Pure and Applied Chemistry backbone-torsion angles.Log-odds ratio: log-odds ratio is a statistical feature calculated by DiscoTope.Depth index: the PSAIA program was used to calculate a series of features for depth index, including the average depth index (denoted as ave_dpx), standard deviation of the depth index (sd_dpx), side-chain average dep […]

library_books

Prediction of protein–protein interaction sites by means of ensemble learning and weighted feature descriptor

2016
PMCID: 4943499
PMID: 27437195
DOI: 10.1186/s40709-016-0046-7

[…] us, the feature vector components were arranged in ascending order according to the distance between the neighboring residues, which can be defined as follows, (V=VD,VI,VQ,VS,VA),where Vresidue=(HSSP,PSAIA,HIQ,AAFactors),residue=D,I,Q,S,A.Second, we calculate the distance effect according to Cα-atom coordinate of D, I, Q, S and A. Here, the Euclidean distance is used to evaluate the distance effec […]

library_books

Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron ion interaction pseudopotential features

2016
Oncotarget
PMCID: 4951271
PMID: 26934646
DOI: 10.18632/oncotarget.7695

[…] 55 structure-based features related to accessible surface area (ASA), relative ASA (RASA), depth index (DI), and protrusion index (PI) were used in this study. These features were calculated using PSAIA []. For details, please refer to our previous works [, ]. […]

library_books

Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation

2013
PLoS One
PMCID: 3859641
PMID: 24349449
DOI: 10.1371/journal.pone.0083167

[…] rom the PhosphoSitePlus® database [] as the positive control in the RSA analysis 2 alternative accessibility parameters, i.e. the protrusion index CX and the depth index DPX [], were calculated using PSAIA []. By calculation, each atom in a residue was assigned with one pair of CX and DPX. We chose the maximum CX value and the average DPX value for a residue to depict its protrusion and depth due […]

Citations

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PSAIA funding source(s)
This work is funded by Croatian Ministry of science, education and sports grant 119-0982913-1211, grant 036-0362214-1987 and grant 098-1191344-2860.

PSAIA review

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Sayoni Das

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Desktop
Very useful tool to calculate geometric features in protein structures such as depth index and protrusion index.