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Reduction, alignment and visualisation of large diverse sequence families

William R. Taylor
2016 BMC Bioinformatics  
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

Guilhem Faure, Aurélie Bornot, Alexandre G. de Brevern
2008 Biochimie  
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

Dimitrios Vlachakis, Alexandros Armaos, Ioannis Kasampalidis, Arianna Filntisi, Sophia Kossida
2014 International Conference on Algorithms for Big Data  
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

Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern
2019 Source Code for Biology and Medicine  
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

J. Gracy, P. Argos
1998 Bioinformatics  
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]

Sheng Wang
2010 arXiv   pre-print
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

Agnel Praveen Joseph, N. Srinivasan, Alexandre G. de Brevern
2011 Biochimie  
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

Marwa Mohammed M. Ghareeb, Ahmed Sharaf Eldin, Taysir Hassan A. Soliman, Mohammed Ebrahim Marie
2013 Zenodo  
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

Carlos Fernandez-Lozano, Rubén F. Cuiñas, José A. Seoane, Enrique Fernández-Blanco, Julian Dorado, Cristian R. Munteanu
2015 Journal of Theoretical Biology  
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

Peter L Chang, Andrew W Rinne, T Gregory Dewey
2006 BMC Bioinformatics  
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

Helena Cristina G Leitão, Luciana S Pessôa, Jorge Stolfi
2005 Genetics and Molecular Research  
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]

Jiaan Yang, Wei-Hua Lee
2012 Protein Structure  
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]

Leon French, Alioune Ngom, Luis Rueda
2005 Lecture Notes in Computer Science  
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

C. De Filippo, M. Ramazzotti, P. Fontana, D. Cavalieri
2012 Briefings in Bioinformatics  
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

H.E. Williams, J. Zobel
2002 IEEE Transactions on Knowledge and Data Engineering  
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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