Biomedical subjects

Volker A Eyrich

Publications and source records attributed to Volker A Eyrich.

5 recordsLinked to original sources

PubMed2005

EVAcon: a protein contact prediction evaluation service.

Here we introduce EVAcon, an automated web service that evaluates the performance of contact prediction servers. Currently, EVAcon is monitoring nine servers, four of which are specialized in contact prediction and five are general structure prediction servers. Results are compared for all newly determined experimental structures deposited into PDB ( approximately 5-50 per week). EVAcon allows for a precise comparison of the results based on a system of common protein subsets and the commonly accepted evaluation criteria that are also used in the corresponding category of the CASP assessment. EVAcon is a new service added to the functionality of the EVA system for the continuous evaluation of protein structure prediction servers. The new service is accesible from any of the three EVA mirrors: PDG (CNB-CSIC, Madrid) (http://www.pdg.cnb.uam.es/eva/con/index.html); CUBIC (Columbia University, NYC) (http://cubic.bioc.columbia.edu/eva/con/index.html); and Sali Lab (UCSF, San Francisco) (http://eva.compbio.ucsf.edu/~eva/con/index.html).

Amino Acids↗

PubMed2005

System for accepting server predictions in CASP6.

We describe the new CASP system for collecting and verifying predictions generated by servers. The system was developed to ensure reliable execution of the server assessment part of CASP, with particular emphasis on data consistency. Following the principle that predictions should not be modified by anyone but their authors and to allow a later meaningful assessment, submissions are now verified for correctness of format and contents within the strict 48 hour CASP deadlines for this type of submission. This article also provides an overview of the rules governing server participation in CASP6 and some statistics pertaining to servers in CASP6.

Automation↗

PubMed2003

META-PP: single interface to crucial prediction servers.

The META-PP server (http://cubic.bioc.columbia.edu/meta/) simplifies access to a battery of public protein structure and function prediction servers by providing a common and stable web-based interface. The goal is to make these powerful and increasingly essential methods more readily available to nonexpert users and the bioinformatics community at large. At present META-PP provides access to a selected set of high-quality servers in the areas of comparative modelling, threading/fold recognition, secondary structure prediction and more specialized fields like contact and function prediction.

Internet↗

PubMed2003

EVA: Evaluation of protein structure prediction servers.

EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods. EVA currently assesses servers for secondary structure prediction, contact prediction, comparative protein structure modelling and threading/fold recognition. Every day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent to the servers and their predictions are collected. The predictions are then compared to the experimental structures once a week; the results are published on the EVA web pages. Over time, EVA has accumulated prediction results for a large number of proteins, ranging from hundreds to thousands, depending on the prediction method. This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods.

Automation↗

PubMed2003

CAFASP3 in the spotlight of EVA.

We have analysed fold recognition, secondary structure and contact prediction servers from CAFASP3. This assessment was carried out in the framework of the fully automated, web-based evaluation server EVA. Detailed results are available at http://cubic.bioc.columbia.edu/eva/cafasp3/. We observed that the sequence-unique targets from CAFASP3/CASP5 were not fully representative for evaluating performance. For all three categories, we showed how careless ranking might be misleading. We compared methods from all categories to experts in secondary structure and contact prediction and homology modellers to fold recognisers. While the secondary structure experts clearly outperformed all others, the contact experts appeared to outperform only novel fold methods. Automatic evaluation servers are good at getting statistics right and at using these to discard misleading ranking schemes. We challenge that to let machines rule where they are best might be the best way for the community to enjoy the tremendous benefit of CASP as a unique opportunity for brainstorming.

Algorithms↗