InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

Quignot, Chloé; Rey, Julien; Yu, Jinchao; Tufféry, Pierre; Guérois, Raphaël; Andréani, Jessica

doi:10.1093/nar/gky377

Cited by 56 publications

(53 citation statements)

References 51 publications

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“…Modelers would need to disentangle intrachain from interchain contacts in the matrix and adapt their pipelines to fold multiple chains according to the given stoichiometry. Previous work has had some success in the heteromeric case but to our knowledge, there is no such studies for the homomeric case.…”

Section: Resultsmentioning

confidence: 99%

Assessment of protein assembly prediction in CASP13

et al. 2019

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We present the assembly category assessment in the 13th edition of the CASP community‐wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches where subunits are modeled in the context of the assemblies they form.

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Section: Resultsmentioning

confidence: 99%

Assessment of protein assembly prediction in CASP13

et al. 2019

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“…In parallel to the identification of the residues involved in the interaction between IN-CTD and mLysRS by experimental methods, we set up an independent docking simulation to explore the most likely interface which could be identified using the InterEvDock2 server [ 27 ] and a refinement protocol based on Rosetta software [ 34 ] (see Mat & Met). We did not use any of the experimental constraint a priori to guide the docking.…”

Section: Resultsmentioning

confidence: 99%

How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-tRNA Synthetase

Phongsavanh

Al-Qatabi

Shaban

et al. 2020

Viruses

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Replication of human immunodeficiency virus type 1 (HIV-1) requires the packaging of tRNALys,3 from the host cell into the new viral particles. The GagPol viral polyprotein precursor associates with mitochondrial lysyl-tRNA synthetase (mLysRS) in a complex with tRNALys, an essential step to initiate reverse transcription in the virions. The C-terminal integrase moiety of GagPol is essential for its association with mLysRS. We show that integrases from HIV-1 and HIV-2 bind mLysRS with the same efficiency. In this work, we have undertaken to probe the three-dimensional (3D) architecture of the complex of integrase with mLysRS. We first established that the C-terminal domain (CTD) of integrase is the major interacting domain with mLysRS. Using the pBpa-photo crosslinking approach, inter-protein cross-links were observed involving amino acid residues located at the surface of the catalytic domain of mLysRS and of the CTD of integrase. In parallel, using molecular docking simulation, a single structural model of complex was found to outscore other alternative conformations. Consistent with crosslinking experiments, this structural model was further probed experimentally. Five compensatory mutations in the two partners were successfully designed which supports the validity of the model. The complex highlights that binding of integrase could stabilize the tRNALys:mLysRS interaction.

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“…Examples include ClusPro, 101 GRAMM-X, 102 PatchDock, 103 SwarmDock, 104 pyDockWEB, 105 GalaxyTongDock, 106 and InterEvDock2. 107 This feature is especially useful in cases where experimental data are available. 87 Interface residue predictions, especially those mentioned above that use conservation or coevolution (Figure 3, label 3), can also be used as restraints in the docking process (Figure 3, label 4).…”

Section: Use Of Conservation In Free and Guided Dockingmentioning

confidence: 99%

“…InterEvScore was integrated in the recently updated free docking server InterEvDock2. 107 InterEvDock2 generates decoys using FRODOCK2 114 and returns the best interface models using a consensus of three different scores: coevolution-based InterEvScore, FRODOCK's mainly physics-based score and an atomic-detail statistical potential score, SOAP-PP. 115 This consensus scoring was shown to improve the success rate on a large test set of 812 protein complexes from the PPI4DOCK database that have available evolutionary information.…”

Section: Use Of Coevolution To Score Docking Decoysmentioning

confidence: 99%

Structural prediction of protein interactions and docking using conservation and coevolution

Andréani

Quignot

Guérois

2020

WIREs Comput Mol Sci

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Knowledge of the detailed structure of macromolecular interactions is key to a better understanding and modulation of essential cellular functions and pathological situations. Great efforts are invested in the development of improved computational prediction methods, including binding site prediction and protein-protein docking. These tools should benefit from the inclusion of evolutionary information, since the pressure to maintain functional interactions leads to conservation signals on protein surfaces at interacting sites and coevolution between contacting positions. However, unveiling such constraints and finding the best way to integrate them into computational pipelines remains a challenging area of research. Here, we first introduce evolutionary properties of interface structures, focusing on recent work exploring evolutionary mechanisms at play in protein interfaces and characterizing the complexity of evolutionary signals, such as interface deep mutational scans. Then, we review binding site predictors and interface structure modeling methods that integrate conservation and coevolution as important ingredients to improve predictive capacity, ending with a section dedicated to the prediction of binding modes between a globular protein domain and a short motif located within an intrinsically disordered or flexible region. Throughout the review, we discuss practical applications and recent promising developments, in particular regarding the use of coevolutionary information for interface structural prediction and the integration of these coevolution signals with machine learning and deep learning algorithms.

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InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

Cited by 56 publications

References 51 publications

Assessment of protein assembly prediction in CASP13

Assessment of protein assembly prediction in CASP13

How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-tRNA Synthetase

Structural prediction of protein interactions and docking using conservation and coevolution

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