FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.
In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts.
Kosinski
Jan
J
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Gajda
Michal J
MJ
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Cymerman
Iwona A
IA
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Kurowski
Michal A
MA
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Pawlowski
Marcin
M
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Boniecki
Michal
M
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Obarska
Agnieszka
A
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Papaj
Grzegorz
G
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Sroczynska-Obuchowicz
Paulina
P
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Tkaczuk
Karolina L
KL
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Sniezynska
Paulina
P
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Sasin
Joanna M
JM
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Augustyn
Anna
A
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Bujnicki
Janusz M
JM
International Institute of Molecular and Cell Biology, Warsaw, Poland.
Feder
Marcin
M
International Institute of Molecular and Cell Biology, Warsaw, Poland.
D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software