Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. (2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. (3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. (4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. (5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. (6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. (7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas

New encouraging developments in contact prediction: Assessment of the CASP11 results

This article provides a report on the state-of-the-art in the prediction of intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts. Twenty-nine groups participated in contact prediction in CASP11. At least eight of them used the recently developed evolutionary coupling techniques, with the top group (CONSIP2) reaching precision of 27% on target proteins that could not be modeled by homology. This result indicates a breakthrough in the development of methods based on the correlated mutation approach. Successful prediction of contacts was shown to be practically helpful in modeling three-dimensional structures; in particular target T0806 was modeled exceedingly well with accuracy not yet seen for ab initio targets of this size (>250 residues

Critical assessment of methods of protein structure prediction—Round VII

This paper is an introduction to the supplemental issue of the journal PROTEINS, dedicated to the seventh CASP experiment to assess the state of the art in protein structure prediction. The paper describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Highlights are improvements in model accuracy relative to that obtainable from knowledge of a single best template structure; convergence of the accuracy of models produced by automatic servers toward that produced by human modeling teams; the emergence of methods for predicting the quality of models; and rapidly increasing practical applications of the methods

Електронний архів ВНТУ як інформаційний навігатор у світі інтелектуальних ресурсів відкритого доступу

У статті висвітлено питання відкритого доступу до наукової інформації через створення інституційних репозитаріїв ВНЗ. Розглядаються стратегічні напрями створення та розвитку університетського репозитарію Вінницького національного технічного університету, роль Науково-технічної бібліотеки в процесі розвитку електронного архіву, його місце в міжнародному бібліотечно-інформаційному просторі

New tools and expanded data analysis capabilities at the protein structure prediction center

We outline the main tasks performed by the Protein Structure Prediction Center in support of the CASP7 experiment and provide a brief review of the major measures used in the automatic evaluation of predictions. We describe in more detail the software developed to facilitate analysis of modeling success over and beyond the available templates and the adopted Java-based tool enabling visualization of multiple structural superpositions between target and several models/templates. We also give an overview of the CASP infrastructure provided by the Center and discuss the organization of the results web pages available through http://predictioncenter.or

Methods for estimation of model accuracy in CASP12

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 paper, the most successful groups in CASP12 describe their latest methods for Estimates of Model Accuracy (EMA). We show that pure single model accuracy estimation methods have shown clear progress since CASP11; the three top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). While the pure single model accuracy estimation methods outperform quasi-single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb-domain and Wallner) in model selection, they are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact based model quality measures (CAD, lDDT) the single model quality methods perform relatively better

Assessment of protein disorder region predictions in CASP10

A systematic analysis of intrinsic disorder in proteins started at the turn of the century1–4 and still remains a hot research topic.5 Only this year several papers covering general aspects of protein disorder have been published5– 9 and the discussion on the fundamental principles of disorder continues to unfold.10,11 PubMed search with the keywords “intrinsically disordered protein 2012” and “intrinsically disordered protein 2013” returned 525 and 305 entries, respectively (as of April 2013). The number of experimentally verified intrinsically disordered proteins and regions is steadily increasing. The DisProt database12 currently contains annotations for 684 intrinsically disordered proteins, 1513 disordered regions, and describes 38 different biological functions associated with disordered regions. The more recently established IDEAL database also has a number of useful annotations on disordered proteins.13 Such a high interest in this area of research triggered rapid development of computational methods for prediction of the location of disordered regions in proteins. The recently published reviews and assessment papers14–18 altogether provide a comprehensive analysis of more than fifty disorder prediction methods. An independent assessment of the protein disorder methods within the scope of CASP started in 2002 and is now already in its sixth round.18–22 This study analyzes the results obtained by the 28 disorder prediction groups participating in CASP10

Evaluation of template-based models in CASP8 with standard measures

The strategy for evaluating template-based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statistical significance of the differences in scores between prediction methods. These data are made available to the assessor of the template-based modeling category, who uses them as a starting point for further evaluations and analyses. This article describes the detailed workflow of the procedure, provides justifications for a number of choices that are customarily made for CASP data evaluation, and reports the results of the analysis of template-based predictions at CASP8