Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

Huang, Sheng‐You; Grinter, Sam Z.; Zou, Xiaoqin

doi:10.1039/c0cp00151a

Cited by 426 publications

(348 citation statements)

References 131 publications

(205 reference statements)

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“…incremental construction, exhaustive search) 21,22 . The binding energy associated to the different docking poses is calculated through the application of scoring functions (SF) that can be classified into knowledge-based, force field-based and empirical SFs 23,24 . Each of these and other methods implemented in the most popular docking programs has its own strenghts and limitations, therefore there is not a particular algorithm/SF combination outperforming the other ones in terms of reliablity and accuracy.…”

Section: Introductionmentioning

confidence: 99%

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

Poli

Martinelli

Tuccinardi

2016

Journal of Enzyme Inhibition and Medicinal Chemistry

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Ligand-protein docking is one of the most common techniques used in virtual screening campaigns. Despite the large number of docking software available, there is still the need of improving the efficacy of docking-based virtual screenings. To date, only very few studies evaluated the possibility of combining the results of different docking methods to achieve higher success rates in virtual screening studies (consensus docking). In order to better understand the range of applicability of this approach, we carried out an extensive enriched database analysis using the DUD dataset. The consensus docking protocol was then refined by applying modifications concerning the calculation of pose consensus and the combination of docking methods included in the procedure. The results obtained suggest that this approach performs as well as the best available methods found in literature, confirming the idea that this procedure can be profitably used for the identification of new hit compounds.

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Section: Introductionmentioning

confidence: 99%

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

Poli

Martinelli

Tuccinardi

2016

Journal of Enzyme Inhibition and Medicinal Chemistry

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“…The structure is constructed using pairwise potentials derived from known receptor-ligand complexes (Ferreira et al, 2015;Kitchen et al, 2004). This is based on the inverse Boltzmann relation (vide infra), which comes from statistical mechanics and as such involves mean force potentials instead of real ones (Huang, Grinter & Zou, 2010). For example, consider the Equation 4.…”

Section: Knowledge-basedmentioning

confidence: 99%

“…Given the different scopes of scoring functions and algorithms it is expected that they complement each other. However, since scoring functions are constructed with different bases their comparison and combination is not straightforward (Huang, Grinter & Zou, 2010). A first attempt was made by Charifson, Corkery, Murcko & Walters, 1999).…”

Section: Consensus Dockingmentioning

confidence: 99%

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Acoplamiento Molecular: Avances Recientes y Retos

2018

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Nota: Artículo recibido el 18 de octubre de 2017 y aceptado el 02 de mayo de 2018. ARTÍCULO DE REVISIÓN abstractAutomated molecular docking aims at predicting the possible interactions between two molecules. This method has proven useful in medicinal chemistry and drug discovery providing atomistic insights into molecular recognition. Over the last 20 years methods for molecular docking have been improved, yielding accurate results on pose prediction. Nonetheless, several aspects of molecular docking need revision due to changes in the paradigm of drug discovery. In the present article, we review the principles, techniques, and algorithms for docking with emphasis on protein-ligand docking for drug discovery. We also discuss current approaches to address major challenges of docking.Key Words: chemoinformatics, computer-aided drug design, drug discovery, structure-activity relationships. Acoplamiento Molecular: Avances Recientes y Retos resuMenEl acoplamiento molecular automatizado tiene como objetivo proponer un modelo de unión entre dos moléculas. Este método ha sido útil en química farmacéutica y en el descubrimiento de nuevos fármacos por medio del entendimiento de las fuerzas de interacción involucradas en el reconocimiento molecular. Durante los últimos 20 años se ha modificado extensamente la técnica de acoplamiento molecular dando resultados precisos en la predicción de los modos de unión. Sin embargo, hay algunas áreas que requieren ser mejoradas substancialmente. En este trabajo se revisan principios, técnicas y algoritmos usados en los programas computacionales del acoplamiento molecular con enfoque en la interacción proteína-ligando aplicado al descubrimiento de nuevos fármacos. También se discuten las estrategias dirigidas a solucionar los principales retos de esta técnica computacional.Palabras Clave: descubrimiento de nuevos fármacos, diseño de fármacos asistido por computadora, quimioinformática, relaciones estructura-actividad.

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“…Most virtual screening studies are hampered by the selection of the appropriate docking programs or scoring functions based on a single crystal structure [21] . However, proteins are dynamically flexible macromolecules, and different structures of a protein may show different recognition abilities towards even the same ligand.…”

Section: Introductionmentioning

confidence: 99%

Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors

Sun

Chen

et al. 2013

Acta Pharmacol Sin

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Aim: To develop a novel 3D-QSAR approach for study of the epidermal growth factor receptor tyrosine kinase (EGFR TK) and its inhibitors. Methods: One hundred thirty nine EGFR TK inhibitors were classified into 3 clusters. Ensemble docking of these inhibitors with 19 EGFR TK crystal structures was performed. Three protein structures that showed the best recognition of each cluster were selected based on the docking results. Then, a novel QSAR (ensemble-QSAR) building method was developed based on the ligand conformations determined by the corresponding protein structures. Results: Compared with the 3D-QSAR model, in which the ligand conformations were determined by a single protein structure, ensemble-QSAR exhibited higher R2 (0.87) and Q2 (0.78) values and thus appeared to be a more reliable and better predictive model. Ensemble-QSAR was also able to more accurately describe the interactions between the target and the ligands. Conclusion: The novel ensemble-QSAR model built in this study outperforms the traditional 3D-QSAR model in rationality, and provides a good example of selecting suitable protein structures for docking prediction and for building structure-based QSAR using available protein structures.

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Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

Cited by 426 publications

References 131 publications

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

Acoplamiento Molecular: Avances Recientes y Retos

Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors

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