3D-Jury: a simple approach to improve protein structure predictions

Ginalski, Krzysztof; Elofsson, Arne; Fischer, Daniel; Rychlewski, Leszek

doi:10.1093/bioinformatics/btg124

Cited by 684 publications

(616 citation statements)

References 19 publications

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“…First, the FAT domain (named after its occurrence in FRAP, ATM and TRRAP proteins) was shown to bear distant homology to the Tetratricopeptide repeat (TPR) structure. 49 This relationship was evident in their scoring more than 100 by the 3D-Jury method (a consensus algorithm combining the results of various fold recognition methods to improve reliability), 50 well above the authors' confidence threshold of 50. 51 Like the ARM and HEAT repeats mentioned above, the TPR repeats, and by implication the FAT domains, form α/α superhelices.…”

Section: Genomics Of Autophagy In Trypanosomatidsmentioning

confidence: 93%

Autophagy and Related processes in Trypanosomatids: Insights from Genomic and Bioinformatic Analyses

Herman

Gillies²,

Michels³

et al. 2006

Autophagy

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Section: Genomics Of Autophagy In Trypanosomatidsmentioning

confidence: 93%

Autophagy and Related processes in Trypanosomatids: Insights from Genomic and Bioinformatic Analyses

Herman

Gillies²,

Michels³

et al. 2006

Autophagy

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“…The protein sequences are obtained from the SMART (a Simple Modular Architecture Research Tool) database 72 and submitted to ''The Structure Prediction Meta Server'' 73,74 with the option of an automated homology model program ESyPref3D. ESyPref3D is based on a strategy using neural networks to evaluate sequence alignments 75 and uses the MODELLER program 76,77 to build the final structural model.…”

Section: Homology Modeling and Mutated Proteinsmentioning

confidence: 99%

A flexible docking scheme to explore the binding selectivity of PDZ domains

Gerek

Ozkan

2010

Protein Science

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Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å . We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

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“…4A). Thus, a 319 residue construct fusing residues 154-331 to 517-657 was built and analyzed using the Meta Server at the Bio Info Bank Institute (65). The Meta Server sequence alignment (Suppl.…”

Section: Structural Model Of the Xpc Corementioning

confidence: 99%

Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein

et al. 2006

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3D-Jury: a simple approach to improve protein structure predictions

Abstract: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)

Cited by 684 publications

References 19 publications

Autophagy and Related processes in Trypanosomatids: Insights from Genomic and Bioinformatic Analyses

Autophagy and Related processes in Trypanosomatids: Insights from Genomic and Bioinformatic Analyses

A flexible docking scheme to explore the binding selectivity of PDZ domains

Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein

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