MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information.
Sitao Wu,Yang Zhang +1 more
TLDR
A new threading algorithm MUSTER is developed by extending the previous sequence profile–profile alignment method, PPA, which shows a better performance than using the conventional optimization methods based on the PROSUP database.Abstract:
We develop a new threading algorithm MUSTER by extending the previous sequence profile-profile alignment method, PPA. It combines various sequence and structure information into single-body terms which can be conveniently used in dynamic programming search: (1) sequence profiles; (2) secondary structures; (3) structure fragment profiles; (4) solvent accessibility; (5) dihedral torsion angles; (6) hydrophobic scoring matrix. The balance of the weighting parameters is optimized by a grading search based on the average TM-score of 111 training proteins which shows a better performance than using the conventional optimization methods based on the PROSUP database. The algorithm is tested on 500 nonhomologous proteins independent of the training sets. After removing the homologous templates with a sequence identity to the target >30%, in 224 cases, the first template alignment has the correct topology with a TM-score >0.5. Even with a more stringent cutoff by removing the templates with a sequence identity >20% or detectable by PSI-BLAST with an E-value 0.5. Dependent on the homology cutoffs, the average TM-score of the first threading alignments by MUSTER is 5.1-6.3% higher than that by PPA. This improvement is statistically significant by the Wilcoxon signed rank test with a P-value < 1.0 x 10(-13), which demonstrates the effect of additional structural information on the protein fold recognition. The MUSTER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/MUSTER.read more
Citations
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Journal ArticleDOI
I-TASSER: a unified platform for automated protein structure and function prediction
TL;DR: The iterative threading assembly refinement (I-TASSER) server is an integrated platform for automated protein structure and function prediction based on the sequence- to-structure-to-function paradigm.
Journal ArticleDOI
Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Journal ArticleDOI
Template-based protein structure modeling using the RaptorX web server
Morten Källberg,Morten Källberg,Haipeng Wang,Sheng Wang,Jian Peng,Zhiyong Wang,Hui Lu,Jinbo Xu +7 more
TL;DR: This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling.
Journal ArticleDOI
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.
Víctor Quesada,Laura Conde,Neus Villamor,Gonzalo R. Ordóñez,Pedro Jares,Laia Bassaganyas,Andrew J. Ramsay,Sílvia Beà,Magda Pinyol,Alejandra Martínez-Trillos,Mónica López-Guerra,Dolors Colomer,Alba Navarro,Tycho Baumann,Marta Aymerich,María Rozman,Julio Delgado,Eva Giné,Jesús M. Hernández,Marcos González-Díaz,Diana A. Puente,Gloria Velasco,José M.P. Freije,Jose M. C. Tubio,Romina Royo,Josep Lluís Gelpí,Modesto Orozco,David G. Pisano,Jorge Zamora,Miguel Vazquez,Alfonso Valencia,Heinz Himmelbauer,Mònica Bayés,Simon Heath,Marta Gut,Ivo Gut,Xavier Estivill,Armando López-Guillermo,Xose S. Puente,Elias Campo,Carlos López-Otín +40 more
TL;DR: This work provides the first comprehensive catalog of somatic mutations in CLL with relevant clinical correlates and defines a large set of new genes that may drive the development of this common form of leukemia.
Journal ArticleDOI
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.
Dong Xu,Yang Zhang +1 more
TL;DR: A novel program, QUARK, for template‐free protein structure prediction, which can successfully construct 3D models of correct folds in one‐third cases of short proteins up to 100 residues and outperformed the second and third best servers based on the cumulative Z‐score of global distance test‐total scores in the FM category.
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