Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

Oliva, Romina; Chermak, Edrisse; Cavallo, Luigi

doi:10.3390/molecules200712045

Cited by 20 publications

(19 citation statements)

References 51 publications

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“…The development of approaches, which might improve prediction of the RT inhibition using molecular docking [ 85 , 86 , 87 , 88 , 89 ] is another future direction of the molecular docking approaches. We suppose that creation of new methods, which provide the possibility of taking into account small molecules pharmacophores together with docking results might be helpful.…”

Section: Resultsmentioning

confidence: 99%

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review

2018

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Currently, millions of people are living with human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. However, the spread of the HIV-1 resistance to antiviral agents is the major problem in the antiretroviral therapy and medical management of HIV-infected patients. HIV-1 reverse transcriptase (RT) is one of the key viral targets for HIV-1 inhibition. Therefore, the studies on the combatting the HIV resistance that occurs due to the structural changes in RT, are in great demand. This work aims to provide an overview of the state-of-the-art molecular docking approaches applied to the studies of the HIV-1 resistance, associated with RT structure changes. We have reviewed recent studies using molecular docking with mutant forms of RT. The work discusses the modifications of molecular docking, which have been developed to find the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1. The perspectives of the existing algorithms of molecular docking to the studies on molecular mechanisms of resistance and selection of the correct binding poses for the reverse transcriptase inhibitors are discussed.

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Section: Resultsmentioning

confidence: 99%

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review

2018

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“…interface-related properties, and c) template-based modelling (TBM) of complexes. We do not review the docking field as it has been addressed in several other instances [104][105][106][107][108] . Table 2 summarizes all mentioned protein-protein complex structure prediction and characterization methods, as well as a short description for each.…”

Section: B Use Of Evolutionary Information In Structure Predictionmentioning

confidence: 99%

Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence‐Evolutionary Data

Preto

Almeida

Schaarschmidt

et al. 2018

Encyclopedia of Analytical Chemistry

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Structural characterization of proteins and their complexes is a fundamental part in understanding any biological phenomena. Yet, the experimental determination of the threedimensional structure of proteins and their complexes remains a challenging undertaking. In order to complement the experimental approaches, computational methods have been developed based on a variety of algorithms and models to fill the gap between the amount of sequences and structures. In this chapter, we review the most common methodological approaches currently used in the field, highlighting ab initio structure prediction methods and methods for the prediction and structural modelling of protein-protein interfaces. We particularly focus on the use of evolutionary information to guide the modelling process.

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“…Further, it reports interactive 2D and 3D consensus contact maps (i.e. intermolecular contact maps where the conservation of the contacts in the ensemble is reported on a gray scale [16][17][18][19]). Once the general output has been generated, the user can choose to perform additional analyses on single models.…”

Section: Introductionmentioning

confidence: 99%

The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses

et al. 2020

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Background Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind docking experiment. We introduced in the field CONSRANK (CONSensus RANKing), the first pure consensus method. Also available as a web server, CONSRANK ranks docking models in an ensemble based on their ability to match the most frequent inter-residue contacts in it. We have been blindly testing CONSRANK in all the latest CAPRI rounds, where we showed it to perform competitively with the state-of-the-art energy and knowledge-based scoring functions. More recently, we developed Clust-CONSRANK, an algorithm introducing a contact-based clustering of the models as a preliminary step of the CONSRANK scoring process. In the latest CASP13-CAPRI joint experiment, we participated as scorers with a novel pipeline, combining both our scoring tools, CONSRANK and Clust-CONSRANK, with our interface analysis tool COCOMAPS. Selection of the 10 models for submission was guided by the strength of the emerging consensus, and their final ranking was assisted by results of the interface analysis. Results As a result of the above approach, we were by far the first scorer in the CASP13-CAPRI top-1 ranking, having high/medium quality models ranked at the top-1 position for the majority of targets (11 out of the total 19). We were also the first scorer in the top-10 ranking, on a par with another group, and the second scorer in the top-5 ranking. Further, we topped the ranking relative to the prediction of binding interfaces, among all the scorers and predictors. Using the CASP13-CAPRI targets as case studies, we illustrate here in detail the approach we adopted. Conclusions Introducing some flexibility in the final model selection and ranking, as well as differentiating the adopted scoring approach depending on the targets were the key assets for our highly successful performance, as compared to previous CAPRI rounds. The approach we propose is entirely based on methods made available to the community and could thus be reproduced by any user.

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Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

Cited by 20 publications

References 51 publications

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review

Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence‐Evolutionary Data

The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses

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