Zobrazeno 1 - 10
of 10
pro vyhledávání: '"David Menéndez-Hurtado"'
Publikováno v:
Bioinformatics
Motivation Proteins are ubiquitous molecules whose function in biological processes is determined by their 3D structure. Experimental identification of a protein’s structure can be time-consuming, prohibitively expensive and not always possible. Al
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e53eaaa9b3414a6bca3eabb850bd33f3
https://doi.org/10.1093/bioinformatics/btaa714
https://doi.org/10.1093/bioinformatics/btaa714
Autor:
Björn Wallner, Karolis Uziela, Torsten Schwede, Arne Elofsson, David Menéndez-Hurtado, Česlovas Venclovas, Jie Hou, Myong‐Ho Choe, Gabriel Studer, Kliment Olechnovič, Liam J. McGuffin, Ali H. A. Maghrabi, Kun‐Sop Han, Jianlin Cheng
Publikováno v:
Proteins
Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the prog
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0e943df4d69be73e72cbfd974e49a60
https://doi.org/10.1002/prot.25767
https://doi.org/10.1002/prot.25767
Autor:
John Lamb, Arne Elofsson, Mirco Michel, Joanna I. Sulkowska, Aleksandra I. Jarmolinska, David Menéndez-Hurtado
Publikováno v:
Journal of Molecular Biology. 431:2442-2448
At present, about half of the protein domain families lack a structural representative. However, in the last decade, predicting contact maps and using these to model the tertiary structure for these protein families have become an alternative approac
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ab921fe5b0dd42ebd07ed45c82dd003
https://doi.org/10.1016/j.jmb.2019.01.047
https://doi.org/10.1016/j.jmb.2019.01.047
Publikováno v:
bioRxiv
UnpayWall
ORCID
Microsoft Academic Graph
Datacite
UnpayWall
ORCID
Microsoft Academic Graph
Datacite
Protein modeling quality is an important part of protein structure prediction. We have for more than a decade developed a set of methods for this problem. We have used various types of description of the protein and different machine learning methodo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c479b8391c1c87bdb6156a6d07086a06
https://doi.org/10.1002/prot.25492
https://doi.org/10.1002/prot.25492
Publikováno v:
Bioinformatics. 35:2677-2679
Motivation Residue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. H
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ae03701696e26075eed7ab11f213ffff
https://doi.org/10.1093/bioinformatics/bty1036
https://doi.org/10.1093/bioinformatics/bty1036
Publikováno v:
Bioinformatics
MotivationAccurate contact predictions can be used for predicting the structure of proteins. Until recently these methods were limited to very big protein families, decreasing their utility. However, recent progress by combining direct coupling analy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::29d12399343a5b9fe9b33e6842c87cd1
http://europepmc.org/articles/PMC5870574
http://europepmc.org/articles/PMC5870574
Publikováno v:
Current protocols in bioinformatics. 66(1)
In spite of the fact that there has been a significant increase in the number of solved protein structures, structural information is missing for many proteins. Although structural information is codified in the amino acid sequence, computational pre
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6ae6b30506d192b45aadd84c9def49d3
https://pubmed.ncbi.nlm.nih.gov/31063641
https://pubmed.ncbi.nlm.nih.gov/31063641
Autor:
Arne Elofsson, David Menéndez Hurtado, Chen Keasar, Ali H. A. Maghrabi, Balachandran Manavalan, Jooyoung Lee, Björn Wallner, Keehyoung Joo, Liam J. McGuffin, Tomer Sidi, Robert Pilstål, Karolis Uziela, Claudio Mirabello
Publikováno v:
Proteins. 86
Methods to reliably estimate the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this article, the most successful groups in CASP12 describe t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::98478b0c4c4ea76a4253e91120fbbf24
https://pubmed.ncbi.nlm.nih.gov/28975666
https://pubmed.ncbi.nlm.nih.gov/28975666
Publikováno v:
Bioinformatics
Motivation A few years ago it was shown that by using a maximum entropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very lar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5ef5c45037dc1c64594806470e52d4fd
https://pubmed.ncbi.nlm.nih.gov/28535189
https://pubmed.ncbi.nlm.nih.gov/28535189
Publikováno v:
Bioinformatics (Oxford, England). 33(10)
Summary Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b362c8c24152b0075dfec0ba0f641b57
https://pubmed.ncbi.nlm.nih.gov/28052925
https://pubmed.ncbi.nlm.nih.gov/28052925