CASP5 assessment of fold recognition target predictions

Kinch, Lisa N.; Wrabl, James O.; Krishna, S. Sri; Majumdar, Indraneel; Sadreyev, Ruslan I.; Qi, Yuan; Pei, Jimin; Cheng, Hua; Grishin, Nick V.

doi:10.1002/prot.10557

Cited by 93 publications

(92 citation statements)

References 30 publications

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“…CASP5 suggested that 3D-PSSM and FUGUE might no longer be the most successful original fold recognition methods. 40,54 Hence, it remains to be shown that fold recognition without fold can really compete with the best methods that explicitly use 3D information.…”

Section: Fold Recognition Without Folds Competitive With Methods Usinmentioning

confidence: 98%

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Improving Fold Recognition Without Folds

Przybylski

Rost

2004

Journal of Molecular Biology

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Section: Fold Recognition Without Folds Competitive With Methods Usinmentioning

confidence: 98%

“…One of the best non-META methods at CASP5 was ORFeus. 22,40,51 This method uses 1D predictions and explores the full potential of profile-profile alignments. We could not compare ORFeus and AGAPE on identical data sets.…”

Section: Improving Fold Recognition Without Foldsmentioning

confidence: 99%

Improving Fold Recognition Without Folds

Przybylski

Rost

2004

Journal of Molecular Biology

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“…Now existing commercial software Insight II Composer, can complete the modeling function, there are also free terminal similar with Swiss Port, which is possible to achieve this purpose. Chothia C. Et al [6,7] proposed the accuracy of protein homology modeling in 1986, to a large extent depends on the consistency of the selected protein template sequence and the target sequence. However, many model predicts contest (CASP) showed that it is still possible to get the protein model closed to the real structure in low homology [8,9].…”

Section: Prediction Methods Of Protein Structurementioning

confidence: 99%

Application of Computer Modelling in Predicting Endocrine Disrupting Chemicals Functions

Yan

Wang

et al. 2013

2013 Fourth International Conference on Intelligent Systems Design and Engineering Applications

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Crystal structures of proteins are necessary in controlling the mechanism between Endocrine Disrupting Chemicals and protein receptors. However there lacks the researches protein structures delay. The strategy of computing including homology modelling and docking method can be used to fill up the gap. Up to now, homology modelling is the best way to obtain useful structures. Meanwhile docking is used in protein ligand researches. The corresponding computational tools are helpful to carry on the research on the endocrine disrupting mechanism which is triggered by receptor ligand interaction.

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“…Finally, domain boundaries for each region classified in Table 1 were assessed manually, taking into account all components of the performed analysis, which in many cases included 3D-model building. (19). The results of this structure-functional annotation are presented in Table 1 and summarized in Fig.…”

Section: Methodsmentioning

confidence: 99%

Protein structure prediction for the male-specific region of the human Y chromosome

Ginalski

Rychlewski

Baker

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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The complete sequence of the male-specific region of the human Y chromosome (MSY) has been determined recently; however, detailed characterization for many of its encoded proteins still remains to be done. We applied state-of-the-art protein structure prediction methods to all 27 distinct MSY-encoded proteins to provide better understanding of their biological functions and their mechanisms of action at the molecular level. The results of such large-scale structure-functional annotation provide a comprehensive view of the MSY proteome, shedding light on MSY-related processes. We found that, in total, at least 60 domains are encoded by 27 distinct MSY genes, of which 42 (70%) were reliably mapped to currently known structures. The most challenging predictions include the unexpected but confident 3D structure assignments for three domains identified here encoded by the USP9Y, UTY, and BPY2 genes. The domains with unknown 3D structures that are not predictable with currently available theoretical methods are established as primary targets for crystallographic or NMR studies. The data presented here set up the basis for additional scientific discoveries in human biology of the Y chromosome, which plays a fundamental role in sex determination. D ue to an increasing gap between the overwhelming number of available protein sequences and experimentally determined protein structures, protein structure prediction has become an important venue with prolific applications in molecular biology (1). Continuous progress in this field has led to a variety of approaches applicable to structure-functional annotation of proteins. In particular, the recent advances in fold recognition (FR) and ab initio (AI) areas resulted in several methods that can reveal reliable but unexpected links between proteins (2, 3) defying standard approaches such as PSI-BLAST (4). FR͞AI tools offer opportunities to advance annotation of poorly characterized proteins, providing valuable information to guide scientific discoveries.Using a bouquet of state-of-art methods, we propose a coherent, semiautomatic strategy for structure-functional annotation of proteins and apply it to protein sequences encoded by the male-specific region of the human Y chromosome (MSY). For many years this distinctive segment of the human genome, which plays a critical role in sex determination, has been considered a functional wasteland. Complete sequence of the MSY, which comprises 95% of the length of the chromosome, revealed at least 78 protein-coding genes that collectively encode 27 distinct proteins (5). MSY genes participate in diverse processes such as skeletal growth, germ cell tumorigenesis, graft rejection, gonadal sex determination, and spermatogenic failure (6). The biological significance of the MSY has begun to surface in recent years; however, many protein-coding genes await more-detailed studies to understand their exact biological functions at the molecular level (7). Thus, comprehensive structural and functional annotation of the MSY-encoded proteins has a b...

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CASP5 assessment of fold recognition target predictions

Cited by 93 publications

References 30 publications

Improving Fold Recognition Without Folds

Improving Fold Recognition Without Folds

Application of Computer Modelling in Predicting Endocrine Disrupting Chemicals Functions

Protein structure prediction for the male-specific region of the human Y chromosome

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