NDLI: A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Content Provider	PubMed Central
Author	Yan, Renxiang Xu, Dong Yang, Jianyi Walker, Sara Zhang, Yang
Copyright Year	2013
Abstract	Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein fold-recognition on a uniform template library. Results demonstrate dominant advantage of profile-profile based methods, which generate models with average TM-score 26.5% higher than sequence-profile methods and 49.8% higher than sequence-sequence alignment methods. There is no obvious difference in results between methods with profiles generated from PSI-BLAST PSSM matrix and hidden Markov models. Accuracy of profile-profile alignments can be further improved by 9.6% or 21.4% when predicted or native structure features are incorporated. Nevertheless, TM-scores from profile-profile methods including experimental structural features are still 37.1% lower than that from TM-align, demonstrating that the fold-recognition problem cannot be solved solely by improving accuracy of structure feature predictions.
Related Links	http://dx.doi.org/10.1038/srep02619
Starting Page	2619
File Format	PDF
ISSN	20452322
e-ISSN	20452322
Journal	Scientific Reports
Volume Number	3
Language	English
Publisher	Nature Publishing Group
Publisher Date	2013-09-01
Access Restriction	Open
Rights Holder	Nature Publishing Group
Subject Keyword	Science and technology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

A General Framework to Learn Tertiary Structure for Protein Sequence Characterization

LocARNA 2.0: versatile simultaneous alignment and folding of RNAs

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

How frequent are correlated changes in families of protein sequences?

Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence.

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

Factors limiting the performance of prediction-based fold recognition methods.

Protein structure alignment beyond spatial proximity

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Similar Documents

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

A General Framework to Learn Tertiary Structure for Protein Sequence Characterization

LocARNA 2.0: versatile simultaneous alignment and folding of RNAs

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

How frequent are correlated changes in families of protein sequences?

Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence.

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

Factors limiting the performance of prediction-based fold recognition methods.

Protein structure alignment beyond spatial proximity

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction