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A modular perspective of protein structures: application to fragment based loop modeling.
Fernandez-Fuentes N, Fiser A. Fernandez-Fuentes N, et al. Among authors: fiser a. Methods Mol Biol. 2013;932:141-58. doi: 10.1007/978-1-62703-065-6_9. Methods Mol Biol. 2013. PMID: 22987351 Free PMC article.
We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. ...As a first …
We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular seco …
Chaos game representation of protein structures.
Fiser A, Tusnády GE, Simon I. Fiser A, et al. J Mol Graph. 1994 Dec;12(4):302-4, 295. doi: 10.1016/0263-7855(94)80109-6. J Mol Graph. 1994. PMID: 7696222
A further application will be presented for testing structure prediction methods using CGR....
A further application will be presented for testing structure prediction methods using CGR....
Different sequence environments of amino acid residues involved and not involved in long-range interactions in proteins.
Tüdös E, Fiser A, Simon I. Tüdös E, et al. Among authors: fiser a. Int J Pept Protein Res. 1994 Feb;43(2):205-8. doi: 10.1111/j.1399-3011.1994.tb00524.x. Int J Pept Protein Res. 1994. PMID: 8200741
Even a limited amount of information on long-range interactions could help in conformational energy calculations of protein structures and could lead to a better understanding of how the primary structure of proteins determines their conformation. ...By using the si …
Even a limited amount of information on long-range interactions could help in conformational energy calculations of protein structure …
Stabilization centers in proteins: identification, characterization and predictions.
Dosztányi Z, Fiser A, Simon I. Dosztányi Z, et al. Among authors: fiser a. J Mol Biol. 1997 Oct 3;272(4):597-612. doi: 10.1006/jmbi.1997.1242. J Mol Biol. 1997. PMID: 9325115
The most frequent stabilization center residues are usually found at buried positions and have a hydrophobic or aromatic side-chain, but some polar or charged residues also play an important role in the stabilization. ...
The most frequent stabilization center residues are usually found at buried positions and have a hydrophobic or aromatic side-chain, …
Modeling of loops in protein structures.
Fiser A, Do RK, Sali A. Fiser A, et al. Protein Sci. 2000 Sep;9(9):1753-73. doi: 10.1110/ps.9.9.1753. Protein Sci. 2000. PMID: 11045621 Free PMC article.
The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. ...The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a
The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy functi …
Servers for sequence-structure relationship analysis and prediction.
Dosztányi Z, Magyar C, Tusnády GE, Cserzo M, Fiser A, Simon I. Dosztányi Z, et al. Among authors: fiser a. Nucleic Acids Res. 2003 Jul 1;31(13):3359-63. doi: 10.1093/nar/gkg589. Nucleic Acids Res. 2003. PMID: 12824327 Free PMC article.
Tools for comparative protein structure modeling and analysis.
Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Eswar N, et al. Among authors: fiser a. Nucleic Acids Res. 2003 Jul 1;31(13):3375-80. doi: 10.1093/nar/gkg543. Nucleic Acids Res. 2003. PMID: 12824331 Free PMC article.
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relie …
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a progr …
ModLoop: automated modeling of loops in protein structures.
Fiser A, Sali A. Fiser A, et al. Bioinformatics. 2003 Dec 12;19(18):2500-1. doi: 10.1093/bioinformatics/btg362. Bioinformatics. 2003. PMID: 14668246
A user provides the input to the server via a simple web interface, and receives the output by e-mail. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a
A user provides the input to the server via a simple web interface, and receives the output by e-mail. The server relies on th
Protein structure modeling in the proteomics era.
Fiser A. Fiser A. Expert Rev Proteomics. 2004 Jun;1(1):97-110. doi: 10.1586/14789450.1.1.97. Expert Rev Proteomics. 2004. PMID: 15966803 Review.
A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. ...
A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the
A supersecondary structure library and search algorithm for modeling loops in protein structures.
Fernandez-Fuentes N, Oliva B, Fiser A. Fernandez-Fuentes N, et al. Among authors: fiser a. Nucleic Acids Res. 2006 Apr 14;34(7):2085-97. doi: 10.1093/nar/gkl156. Print 2006. Nucleic Acids Res. 2006. PMID: 16617149 Free PMC article.
We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. ...In a head-t …
We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensi …
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