Template‐based protein structure prediction in <scp>CASP11</scp> and retrospect of <scp>I‐TASSER</scp> in the last decade

Yang, Jianyi; Zhang, Wenxuan; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong; Zhang, Yang

doi:10.1002/prot.24918

Cited by 50 publications

(51 citation statements)

References 42 publications

(72 reference statements)

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“…It is noted that if the target is identified as “trivial” or “easy”, based on the significance and consensus of LOMETS threading alignments (as described in Equation of our CASP10 report), the initial structures and distance restraints are obtained from the LOMETS templates, which are also used for guiding the QUARK‐based REMC simulations.…”

Section: Methodsmentioning

confidence: 99%

“…In CASP10 and CASP11, for instance, the interplay between the template‐based I‐TASSER method and the ab initio folding QUARK method has demonstrated enhancements of accuracy of the final models for FM targets . In this approach, the structures of QUARK based models are compared with those of the templates identified by LOMETS, and the templates are re‐ranked based on their similarity to the QUARK models. These templates are then used in the I‐TASSER structure‐assembly simulations to predict the final models.…”

Section: Introductionmentioning

confidence: 99%

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Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Zhang

Mortuza

et al. 2017

Proteins

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We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM-score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non-foldable to foldable (TM-score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue-level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi-domain proteins and folding of β-proteins with complicated topologies bound by long-range strand-strand interactions. Improvements on domain boundary and long-range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Zhang

Mortuza

et al. 2017

Proteins

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“…Robetta server is, with I-TASSER55 server, one of the most powerful and accurate tool for protein structure prediction456575859. However, these servers are based on ab initio and de novo methods, which are more time-consuming.…”

Section: Resultsmentioning

confidence: 99%

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

Ghouzam

Postic

Guérin

et al. 2016

Sci Rep

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Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.

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“…Although full convergence of MREMD simulations was not achieved for multi-domain proteins (T0775, T0793 and T0799) because of the strictly restricted time window for predictions, our models of their domains are very good. In Figure 4, the GDT-TS (Global Distance TestTotal Score) values and RMSDs from the experimental structure of the best models from the Cornell-Gdansk group are compared with the best predictions over all groups participating in CASP11 and with those of the Zhang group, which generally performed best in the CASP11 experiment (Yang et al, 2015) (Fig. 4).…”

Section: General Performance Of the Unres Force Fieldmentioning

confidence: 99%

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

et al. 2016

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Summary: Participating as the Cornell-Gdansk group, we have used our physics-based coarsegrained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six singledomain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CaRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes. Availability and Implementation: Freely available on the web at

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Template‐based protein structure prediction in CASP11 and retrospect of I‐TASSER in the last decade

Cited by 50 publications

References 42 publications

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

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