From Protein Structure to Function with Bioinformatics.pdf

50 L.A. KelleyTable 2.2 Popular web servers for remote homology/fold recognition. ‘Consensus’ indicates theserver collates results from multiple independent servers to form a final prediction, whereas ‘single’indicates a server uses only its own local methods. The Model building/confidence measurecolumn indicates whether a server provides as output 3D coordinates of a potential model(‘Model’) and a score indicating the confidence in the model (Z-score, P-value, E-value, etc.). The‘FR/ab initio’ column indicates whether the server can produce results based only on remotehomology/fold recognition (‘FR’) or can additionally build models in the absence of a template(‘ab initio’)Consensus/singleModel building/confidence measure?Server name Web addressI-TASSER http://zhang.bioinfor-Single Model +matics.ku.edu/I-confidenceTASSER/Phyre http://www.imperial. Single Model +FRac.uk/phyre/confidenceSAM-T06 http://www.soe.ucsc.edu/ Single Model +FRcompbio/SAM_T06/confidenceT06-query.htmlHHpred http://toolkit.tuebingen. Single Confidence FRmpg.de/hhpredGenThreader http://bioinf.cs.ucl.ac.uk/ Single P-value FRpsipred/psiform.htmlPCONS http://pcons.net/ Consensus Model + Pcons score FRBioinfo http://meta.bioinfo.pl Consensus Model + E-value FRFFAS http://ffas.ljcrf.edu Single FFAS score FRRobettaSP 4http://robetta.bakerlab.org/http://sparks.informatics.iupui.edu/SP4/FR/ab initioFR + ab initioSingle Model +FR + ab initioconfidenceSingle Model + Z-score FRdeveloped I-TASSER server, although developed with fold recognition in mind, alsodemonstrated some promise in ab initio modelling at CASP7.The turnaround time for a job on most of these servers is usually less than anhour, with the important caveat that this will be heavily dependent on the numberof jobs in the queue at any one time. The ease of use and interpretation of resultsfrom these systems varies widely and their suitability for a given user will be heavilydependent on their level of experience. In addition, it is always wise to use severalservers when tackling a prediction problem to protect against spurious results.2.6 The FutureNone of the most successful methods in recent CASP competitions have solely utilisedthreading. Many methods use no threading at all, although some use a knowledgebasedpotential to post-screen potential models or in conjunction with profile