2003
Journal Articles
301.
Eckart Bindewald; Alessandro Cestaro; Jürgen Hesser; Matthias Heiler; Silvio C. E. Tosatto
MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification Journal Article
In: Protein Engineering, vol. 16, no. 11, pp. 785-789, 2003, (Cited by: 35).
Abstract | Links:
@article{SCOPUS_ID:0345600222,
title = {MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification},
author = {Eckart Bindewald and Alessandro Cestaro and Jürgen Hesser and Matthias Heiler and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-0345600222&origin=inward},
doi = {10.1093/protein/gzg106},
year = {2003},
date = {2003-01-01},
journal = {Protein Engineering},
volume = {16},
number = {11},
pages = {785-789},
publisher = {Oxford University Press},
abstract = {We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the fold of the target protein. We developed a non-linear ranking scheme in order to combine the scores of the three different similarity measures used. For a difficult test set of proteins with very little sequence similarity, the program predicts the fold class correctly in 34% of cases. This is an over twofold increase in accuracy compared with sequence-based methods such as PSI-BLAST or GenTHREADER, which score 13-14% correct first hits for the same test set. The functional similarity term increases the prediction accuracy by up to 3% compared with using the combination of secondary structure similarity and PSI-BLAST alone. We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity.},
note = {Cited by: 35},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a protein fold recognition method, MANIFOLD, which uses the similarity between target and template proteins in predicted secondary structure, sequence and enzyme code to predict the fold of the target protein. We developed a non-linear ranking scheme in order to combine the scores of the three different similarity measures used. For a difficult test set of proteins with very little sequence similarity, the program predicts the fold class correctly in 34% of cases. This is an over twofold increase in accuracy compared with sequence-based methods such as PSI-BLAST or GenTHREADER, which score 13-14% correct first hits for the same test set. The functional similarity term increases the prediction accuracy by up to 3% compared with using the combination of secondary structure similarity and PSI-BLAST alone. We argue that using functional and secondary structure information can increase the fold recognition beyond sequence similarity.
2002
Journal Articles
302.
Silvio C. E. Tosatto; Eckart Bindewald; Jürgen Hesser; Reinhard Männer
A divide and conquer approach to fast loop modeling Journal Article
In: Protein Engineering, vol. 15, no. 4, pp. 279-286, 2002, (Cited by: 63; Open Access).
Abstract | Links:
@article{SCOPUS_ID:0036096608,
title = {A divide and conquer approach to fast loop modeling},
author = {Silvio C. E. Tosatto and Eckart Bindewald and Jürgen Hesser and Reinhard Männer},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-0036096608&origin=inward},
doi = {10.1093/protein/15.4.279},
year = {2002},
date = {2002-01-01},
journal = {Protein Engineering},
volume = {15},
number = {4},
pages = {279-286},
publisher = {Oxford University Press},
abstract = {We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 Å RMSD for three-residue loops and 3.72 Å RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations.},
note = {Cited by: 63; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 Å RMSD for three-residue loops and 3.72 Å RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations.
1999
Journal Articles
303.
Murgia; Orzan; Polli; Martella; Vinanzi; Leonardi; Arslan; Zacchello
Cx26 deafness: Mutation analysis and clinical variability Journal Article
In: Journal of Medical Genetics, vol. 36, no. 11, pp. 829-832, 1999, (Cited by: 127; Open Access).
Abstract | Links:
@article{SCOPUS_ID:0032727332,
title = {Cx26 deafness: Mutation analysis and clinical variability},
author = {Murgia and Orzan and Polli and Martella and Vinanzi and Leonardi and Arslan and Zacchello},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-0032727332&origin=inward},
doi = {10.1136/jmg.36.11.829},
year = {1999},
date = {1999-01-01},
journal = {Journal of Medical Genetics},
volume = {36},
number = {11},
pages = {829-832},
publisher = {BMJ Publishing Group},
abstract = {Mutations in the gap junction protein connexin 26 (Cx26) gene (GJB2) seem to account for many cases of congenital sensorineural hearing impairment, the reported prevalence being 34-50% in autosomal recessive cases and 10-37% in sporadic cases. The hearing impairment in these patients has been described as severe or profound. We have studied 53 unrelated subjects with congenital non-syndromic sensorineural hearing impairment in order to evaluate the prevalence and type of Cx26 mutations and establish better genotype-phenotype correlation. Mutations in the Cx26 gene were found in 53% of the subjects tested, 35.3% of the autosomal recessive and 60% of the sporadic cases in our series. Three new mutations were identified. The hearing deficit varied from mild to profound even in 35delG homozygotes within the same family. No evidence of progression of the impairment was found. Alterations of the Cx26 gene account for a large proportion of cases of congenital non-syndromic sensorineural deafness, so it seems appropriate to extend the molecular analysis even to subjects with mild or moderate prelingual hearing impairment of unknown cause.},
note = {Cited by: 127; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mutations in the gap junction protein connexin 26 (Cx26) gene (GJB2) seem to account for many cases of congenital sensorineural hearing impairment, the reported prevalence being 34-50% in autosomal recessive cases and 10-37% in sporadic cases. The hearing impairment in these patients has been described as severe or profound. We have studied 53 unrelated subjects with congenital non-syndromic sensorineural hearing impairment in order to evaluate the prevalence and type of Cx26 mutations and establish better genotype-phenotype correlation. Mutations in the Cx26 gene were found in 53% of the subjects tested, 35.3% of the autosomal recessive and 60% of the sporadic cases in our series. Three new mutations were identified. The hearing deficit varied from mild to profound even in 35delG homozygotes within the same family. No evidence of progression of the impairment was found. Alterations of the Cx26 gene account for a large proportion of cases of congenital non-syndromic sensorineural deafness, so it seems appropriate to extend the molecular analysis even to subjects with mild or moderate prelingual hearing impairment of unknown cause.
