NDLI: Toward an improved discrimination of outer membrane proteins using a sequence-based approach.

Please wait, while we are loading the content...

Effects of light environment on the induction of chlorophyll fluorescence in leaves: a comparative study of Tradescantia species of different ecotypes.

Efficiency of neural transmission as a function of synaptic noise, threshold, and source characteristics.

Novel mathematical models for cell-mediated cytotoxicity assays without applying enzyme kinetics but with combinations and probability: bystanders in bulk effector cells influence results of cell-mediated cytotoxicity assays.

Toward an improved discrimination of outer membrane proteins using a sequence-based approach.

Modeling the cell cycle: from deterministic models to hybrid systems.

Invasion dynamics of epidemic with the Allee effect.

Behavioural robustness: a link between distributed mechanisms and coupled transient dynamics.

A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences.

Rebuilding Iberian motorways with slime mould.

Year: 2011 Volume: 104

Year: 2011 Volume: 103

Year: 2010 Volume: 102

Year: 2010 Volume: 101

Year: 2010 Volume: 100

Year: 2010 Volume: 99

Year: 2009 Volume: 98

Year: 2009 Volume: 97

Year: 2009 Volume: 95

Year: 2008 Volume: 94

Year: 2008 Volume: 93

Year: 2008 Volume: 92

Year: 2007 Volume: 90

Year: 2007 Volume: 89

Year: 2006 Volume: 83

Year: 2001 Volume: 61

Toward an improved discrimination of outer membrane proteins using a sequence-based approach.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Liang, Gui-Zhao Ma, Xiu-Yan Li, Yuan-Chao Lv, Feng-Lin Yang, Li
Description	Country affiliation: China Author Affiliation: Liang GZ ( Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Shazheng Street 174#, Chongqing 400044, China. gzliang@cqu.edu.cn)
Abstract	This article offers a novel sequence-based approach to discriminate outer membrane proteins (OMPs). The first step is to use a new representation approach, factor analysis scales of generalized amino acid information (FASGAI) representing hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility and electronic properties, etc., to characterize sequences of OMPs and non-OMPs. The subsequent data is then transformed into a uniform matrix by the auto cross covariance (ACC). The second step is to develop discrimination predictors of OMPs from non-OMPs using a support vector machine (SVM). The SVM predictors thus successfully produce a high Matthews correlation coefficient (MCC) of 0.916 on 208 OMPs from non-OMPs including 206 -helical membrane proteins and 673 globular proteins by a fivefold cross validation test. Meanwhile, overall MCC values of 0.923 and 0.930 are obtained for the discrimination OMPs from the -helical membrane proteins and the globular proteins, respectively. The results demonstrate that the FASGAI-ACC-SVM combination approach shows great prospect of application in the field of bioinformatics or proteomics studies.
File Format	HTM / HTML
ISSN	03032647
Issue Number	1
Volume Number	105
e-ISSN	18728324
Journal	Biosystems
Language	English
Publisher	Elsevier
Publisher Date	2011-07-01
Publisher Place	Ireland
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Computational Biology Bacterial Outer Membrane Proteins Chemistry Sequence Analysis, Protein Methods Computational Biology Factor Analysis, Statistical Membrane Proteins Protein Structure, Secondary Protein Structure, Tertiary Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Statistics and Probability Medicine Biochemistry, Genetics and Molecular Biology Modeling and Simulation

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information.

Spectral density ratio based clustering methods for the binary segmentation of protein sequences: a comparative study.

Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA.

Solution structure of a bacterial immunoglobulin-like domain of the outer membrane protein (LigB) from Leptospira

Structure-based prediction reveals capping motifs that inhibit ß-helix aggregation.

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.

Structure and Function of the Escherichia coli Tol-Pal Stator Protein $TolR^{*}$

Transmembrane domain of surface-exposed outer membrane lipoprotein RcsF is threaded through the lumen of ß-barrel proteins.

The bacterial outer membrane ß-barrel assembly machinery.

Toward an improved discrimination of outer membrane proteins using a sequence-based approach.

Similar Documents

Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information.

Spectral density ratio based clustering methods for the binary segmentation of protein sequences: a comparative study.

Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA.

Solution structure of a bacterial immunoglobulin-like domain of the outer membrane protein (LigB) from Leptospira

Structure-based prediction reveals capping motifs that inhibit ß-helix aggregation.

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.

Structure and Function of the Escherichia coli Tol-Pal Stator Protein $TolR^{*}$

Transmembrane domain of surface-exposed outer membrane lipoprotein RcsF is threaded through the lumen of ß-barrel proteins.

The bacterial outer membrane ß-barrel assembly machinery.

Toward an improved discrimination of outer membrane proteins using a sequence-based approach.