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Reduction, alignment and visualisation of large diverse sequence families
2016
BMC Bioinformatics
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Results: A method (MULSEL) is presented that combines fast peptide-based pre-sorting with a following cascade of mini-alignments, each of which are generated with a robust profile/profile method. ...
It is often quite difficult to tell from these raw results whether the search has been a success or has picked-up sequences with little or no relationship to the query. ...
The data was designed so that all sequences that are enriched in the same amino acid can be aligned with each other but not with a sequence that has been enriched with a different amino acid type. ...
doi:10.1186/s12859-016-1059-9
pmid:27484804
pmcid:PMC4971687
fatcat:i5zsfgtin5cl5au5yddepyle2y
Protein contacts, inter-residue interactions and side-chain modelling
2008
Biochimie
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First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted. ...
In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria. ...
AB benefits from a grant of the Ministère de la Recherche. ...
doi:10.1016/j.biochi.2007.11.007
pmid:18086572
fatcat:px57zfnbrbcqrbenkkhey3hhgm
ASSP; the Antibody Secondary Structure Profile search tool
2014
International Conference on Algorithms for Big Data
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In this direction, a novel platform has been developed, which is capable of performing a customized hydropathy blast using traditional sequence blast filtering and an integrated fast similarity search ...
However, one of the major drawbacks of modern bioinformatics is the fact that protein similarity and blast searches are still based on primary amino acid sequence rather than structural data. ...
The realization that protein sequence contains hydropathy patterns led to the development of reduced amino acid alphabets based on hydropathy for the prediction of secondary structure. ...
dblp:conf/icabd/VlachakisAKFK14
fatcat:aggyzj2rajc4lgvjg7kmyjzh64
iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach
2019
Source Code for Biology and Medicine
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We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent ...
Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. ...
GF, APJ, NS, JR, JCG and AGdB wrote the manuscript with input from all authors. All authors approved the final manuscript for publication. ...
doi:10.1186/s13029-019-0075-3
pmid:31700529
pmcid:PMC6825713
fatcat:x3dqoo4osvdf5ckpjeior5xgiq
Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
1998
Bioinformatics
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Global similarities are detected from the pairwise comparison of amino acid and dipeptide compositions of each protein. ...
Sets of proteins which share similar sequence segments are then weighted according to their closeness and multiply aligned using a fast hierarchical dynamic programming algorithm. ...
Acknowledgement This work was supported by a grant from the European Union Biomed and Human Capital and Mobility Program. ...
doi:10.1093/bioinformatics/14.2.164
pmid:9545449
fatcat:2zkka3diejc5fbkze632rv77fa
Hydropathy Conformational Letter and its Substitution Matrix HP-CLESUM: an Application to Protein Structural Alignment
[article]
2010
arXiv
pre-print
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Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). ...
Combined with our SA, namely conformational letter (CL) of 17 alphabets, we get a joint alphabet called hydropathy conformational letter (hp-CL). ...
Amino acids (AA) or all kinds of SAs can be treated as coding systems, so long as the alphabet has its substitution matrix. ...
arXiv:1001.2879v2
fatcat:cdcc6qh7sndk3jcrorg6kmphfu
Improvement of protein structure comparison using a structural alphabet
2011
Biochimie
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Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality ...
A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. ...
In conclusion, iPBA (improved PBALIGN approach) provides a fast and efficient means for recognizing protein domains with same fold as the query from a large databank. ...
doi:10.1016/j.biochi.2011.04.010
pmid:21569819
fatcat:jscdjmpmejbaxohxxq7e5zppey
A Deeply Glimpse into Protein Fold Recognition
2013
Zenodo
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The rapid growth in genomic and proteomic data causes a lot of challenges that are raised up and need powerful solutions. ...
Researchers have examined the use of a lot of techniques such as neural networks, Monte Carlo, support vector machine and data mining techniques. ...
To deal with that, researchers have attempted to reduce the search space by simplifying models or reducing the conformation space. ...
doi:10.5281/zenodo.3348233
fatcat:sui7cakaaraqdh2a6pifgzrdmm
Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models
2015
Journal of Theoretical Biology
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2019 pre-print arXiv:1904.05052v1 fatcat:afiimvd6xbc6zmthdvlydwkwxu
Important signaling pathways are presented for three UniprotIDs (34 PDBs) with a signaling prediction greater than 98.0%. ...
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases ...
The standard method to create a Star Graph consists of the next steps: each amino acid/vertex holds the position in the original sequence and the branches are labeled alphabetically by the 3-letter amino ...
doi:10.1016/j.jtbi.2015.07.038
pmid:26297890
fatcat:baktblpytvgvla6bsdxrloai2m
Structure alignment based on coding of local geometric measures
2006
BMC Bioinformatics
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This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. ...
By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. ...
The authors thank valuable discussion with Dr. Eric Scheeff and Dr. Phil Bourne and appreciate their sharing of the multiple alignment data. ...
doi:10.1186/1471-2105-7-346
pmid:16842622
pmcid:PMC1559724
fatcat:uhspbwbvgrhoxila4frwhpsm7m
Mutual information content of homologous DNA sequences
2005
Genetics and Molecular Research
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The necessary information to reproduce and keep an organism is codified in acid nucleic molecules. ...
In the present study, we analyzed the quantity of information contained in a DNA sequence that can be useful to identify sequences homologous to it. ...
Homology search can be formally modeled as follows: the databank is a set of sequences over some alphabet Σ, and the goal is to find the substrings of those sequences that match a given string, within ...
pmid:16342040
fatcat:wzozxbq6szfxjly4wakehkf6xa
Protein Structure Alphabetic Alignment
[chapter]
2012
Protein Structure
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The Polar group of amino acids is divided into properties. Amino acid with hydroxyl group -OH: O, with carbonyl and amide group O=CNH2: N Geom: geometric size and characteristic of amino acid. ...
Introduction This study presents a fast approach to compare protein 3D structures with protein structure alphabetic alignment method. ...
Protein Structure Alphabetic Alignment, Protein Structure, Dr. ...
doi:10.5772/38063
fatcat:brasvx7ownfk7kravnrqmljlmq
Fast Protein Superfamily Classification Using Principal Component Null Space Analysis
[chapter]
2005
Lecture Notes in Computer Science
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Exchange grams are similar but are based on a many-to-one translation of the amino acid alphabet into a six letter alphabet that represents six groups of amino acids, which represent high evolutionary ...
Exchange grams are similar but are based on a many-to-one translation of the amino acid alphabet into a six letter alphabet that represents six groups of amino acids, which represent high evolutionary ...
From the view o f a computer scientist a protein sequence is just a string made up of a 21 letter alphabet (amino acids). ...
doi:10.1007/11424918_17
fatcat:tnwyuhjjyzabzphdoefzg3frgi
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data
2012
Briefings in Bioinformatics
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The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins ...
Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. ...
Another possibility is to scan protein databases such as NCBI nr (non-redundant) with fast, specifically designed protein search tools such as RAPsearch2 [48] that use reduced amino acid alphabets (by ...
doi:10.1093/bib/bbs070
pmid:23175748
pmcid:PMC3505041
fatcat:rm3rv7rp3nht7jyqxkurirfcl4
Indexing and retrieval for genomic databases
2002
IEEE Transactions on Knowledge and Data Engineering
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Amino-acid and nucleotide databases are increasing in size exponentially, and mean sequence lengths are also increasing. ...
We present an index-based approach for both selecting sequences that display broad similarity to a query and for fast local alignment. ...
Availability The index-based gapped search system (cafe) is available free of charge by request to the authors. ...
doi:10.1109/69.979973
fatcat:rhb3572ocjhcnj4ymv5e6dir7y
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