Improving the quality of protein structure models by selecting from alignment alternatives

Sommer, Iris E.; Toppo, Stefano; Sander, Oliver; Lengauer, Thomas; Tosatto, Silvio C. E.

doi:10.1186/1471-2105-7-364

Cited by 18 publications

(12 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A structural template for BsRBL was found by MANIFOLD (Bindewald et al 2003). The alignment was generated by systematic parameter variation (Sommer et al 2006) and visualised with ESPript (Gouet et al 1999). Models for the BsRBL monomer and dimer were constructed with the HOMER server (URL: http://protein.bio.unipd.it/homer/).…”

Section: Bsrbl Structure Analysismentioning

confidence: 99%

Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri

et al. 2011

View full text Add to dashboard Cite

Section: Bsrbl Structure Analysismentioning

confidence: 99%

Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri

et al. 2011

View full text Add to dashboard Cite

“…Sequence conservation was mapped onto the three-dimensional structure using Consurf 32 . The mutant models for eight mutations were built with ClustAlign 41 and HOMER ( http://protein.bio.unipd.it/homer/ ). GROMACS 4.6.5 42 was used for 1,000 steps of steepest descent minimization to relax the mutant structures.…”

Section: Methodsmentioning

confidence: 99%

Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans

Minervini

Quaglia

Tosatto

2016

Sci Rep

Self Cite

View full text Add to dashboard Cite

Idiopathic erythrocytosis is a rare disease characterized by an increase in red blood cell mass due to mutations in proteins of the oxygen-sensing pathway, such as prolyl hydroxylase 2 (PHD2). Here, we present a bioinformatics investigation of the pathological effect of twelve PHD2 mutations related to polycythemia insurgence. We show that few mutations impair the PHD2 catalytic site, while most localize to non-enzymatic regions. We also found that most mutations do not overlap the substrate recognition site, suggesting a novel PHD2 binding interface. After a structural analysis of both binding partners, we suggest that this novel interface is responsible for PHD2 interaction with the LIMD1 tumor suppressor.

show abstract

“…10 We found a particularly strong correlation between the three measures on a set of CASP7 models: r 2 GDT,MaxSub = 0.99, r 2 GDT,TM = 0.99, and r 2 MaxSub,TM = 0.99. The Z-scores used in the CASP benchmark also correlate well: r 2 Z-GDT,Z-MaxSub = 0.99, r 2 Z-GDT,Z-TM = 0.91, and r 2 Z-MaxSub,Z-TM = 0.91.…”

Section: Introductionmentioning

confidence: 93%

A Different Look at the Quality of Modeled Three-Dimensional Protein Structures

Poleksić

Fienup

Danzer³

et al. 2008

J. Bioinform. Comput. Biol.

View full text Add to dashboard Cite

Measuring the accuracy of protein three-dimensional structures is one of the most important problems in protein structure prediction. For structure-based drug design, the accuracy of the binding site is far more important than the accuracy of any other region of the protein. We have developed an automated method for assessing the quality of a protein model by focusing on the set of residues in the small molecule binding site. Small molecule binding sites typically involve multiple regions of the protein coming together in space, and their accuracy has been observed to be sensitive to even small alignment errors. In addition, ligand binding sites contain the critical information required for drug design, making their accuracy particularly important. We analyzed the accuracy of the binding sites on two sets of protein models: the predictions submitted by the top-performing CASP7 groups, and the models generated by four widely used homology modeling packages. The results of our CASP7 analysis significantly differ from the previous findings, implying that the binding site measure does not correlate with the traditional model quality measures used in the structure prediction benchmarks. For the modeling programs, the resolution of binding sites is extremely sensitive to the degree of sequence homology between the query and the template, even when the most accurate alignments are used in the homology modeling process.

show abstract

Improving the quality of protein structure models by selecting from alignment alternatives

Cited by 18 publications

References 31 publications

Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri

Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri

Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans

A Different Look at the Quality of Modeled Three-Dimensional Protein Structures

Contact Info

Product

Resources

About