FOLDpro

[…] tertiary structure prediction was performed by three methods including modeller (http://salilab.org/modeller/), tasser (http://zhanglab.ccmb.med.umich.edu/i-tasser/), and foldpro (http://mine10.ics.uci.edu/). the stability of produced structural models was analyzed by pymol and swiss-pdbviewer. evaluation of model stability was performed based on energy minimization […]

[…] package (dnastar)., to approximate an accurate tertiary model of the s. mansoni glucose transporters sgtp1, sgtp2, sgtp3 and sgtp4 we used several protein structure prediction servers, namely foldpro [], i-tasser [], 3d-jigsaw [], loopp [], phyre2 [] and swissmodel []. to assess the quality of the output models and to choose the top candidates we used resprox [], qmean [], modfold []. […]

[…] of the phylogenetic tree was performed with treedyn (v 198.3) []., to approximate an accurate tertiary model of the an. coluzzii protein, we used several protein structure prediction servers, namely foldpro [], i-tasser [], 3d-jigsaw, loopp [], rosetta [], phyre2 [] and swissmodel []. to assess the quality of the output models and to choose the top candidates, we used resprox [], qmean [], […]

[…] the fold recognition sensitivities between fr-t5 and the existing 9 threading methods that demonstrated good performance in previous casps, namely samt98 , fugue , raptor , sparks , hhpred , foldpro , sp3 , sp4 , sp5 . shows that in terms of fold recognition sensitivity, fr-t5 is comparable to the best of these existing 9 threading methods in finding structural templates for proteins […]

[…] also taking correlated mutation information into consideration., to evaluate the performance of the proposed consensus method, six threading-based protein structure prediction servers are used: foldpro [], mgenthreader [,], raptor [,], fugue3 [], sam-t02 [], and spark3 []. although there are some servers, such as rosetta and zhang-server, with a better performance than that of the six […]

[…] uses the best template, the multi-template approach yields only slightly better performance. during the casp7 experiment, the preliminary implementation of the multi-template combination algorithm (foldpro) was ranked second among 67 servers in the category of high-accuracy structure prediction in terms of gdt-ts measure., we have developed a novel multi-template algorithm to improve protein […]