QA-RecombineIt: a server for quality assessment and recombination of protein models

Abstract

QA-RecombineIt provides a web interface to assess the quality of protein 3D structure models and to improve the accuracy of models by merging fragments of multiple input models. QA-RecombineIt has been developed for protein modelers who are working on difficult problems, have a set of different homology models and/or de novo models (from methods such as I-TASSER or ROSETTA) and would like to obtain one consensus model that incorporates the best parts into one structure that is internally coherent. An advanced mode is also available, in which one can modify the operation of the fragment recombination algorithm by manually identifying individual fragments or entire models to recombine. Our method produces up to 100 models that are expected to be on the average more accurate than the starting models. Therefore, our server may be useful for crystallographic protein structure determination, where protein models are used for Molecular Replacement to solve the phase problem. To address the latter possibility, a special feature was added to the QA-RecombineIt server. The QA-RecombineIt server can be freely accessed at http://iimcb.genesilico.pl/qarecombineit/.

New insights into the structural dynamics of the kinase JNK3

“…The initial models were generated by using the GeneSilico metaserver 52 , Robetta 53 , Quark 54 , HHpred 55 and Multicom server 56 . The outputs of these servers were then submitted to the QA-recombineIt server 57 . The best models were selected based on the ranking provided by the inbuilt ‘Model Quality Assessment Programs’.…”

An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat

“…For model refinement an iterative procedure consisting in global simulated annealing with harmonic restraints on backbone atoms found in definite secondary structure states, followed by model quality assessment with MetaMQAP (Pawlowski et al, 2013). In order to optimize the HvLEMK1-LRR scaffold the Joint Fragment Remote Homology Modeling procedure (Sela et al, 2012; Slootweg et al, 2013) had to be used.…”

Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2

“…The simulation used the CHARMM36 force field and was performed in implicit solvent for 10 ns with harmonic position restraints on the backbone of the protein in regions of secondary structure, whereas the loops were left to move freely so as to eliminate steric conflicts and bring the model to a lower energy minimum. The model was validated using the QA RecombineIT method for quality assessment (37).…”