Molecular Docking Algorithms

Dias, Raquel; Azevedo, Walter Filgueira de

doi:10.2174/138945008786949432

Cited by 181 publications

(77 citation statements)

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“…The process continues until the entire ligand has been constructed. The algorithm performs the conformational search only for the fragments being added, reducing the degrees of freedom to be explored, and thereby avoiding combinatorial explosion [33]. Genetic algorithms (GA) are an interesting application of the stochastic search, which have been successfully used in molecular docking programs such as AutoDock and Gold [34,35].…”

Section: Conformational Searchmentioning

confidence: 99%

Molecular Docking and Structure-Based Drug Design Strategies

et al. 2015

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Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure-and ligand-based methods.

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Section: Conformational Searchmentioning

confidence: 99%

Molecular Docking and Structure-Based Drug Design Strategies

et al. 2015

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“…evolutionary and Monte Carlo algorithms) or systematic search methods (e.g. 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 .…”

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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“…This is made to test if the docking algorithm produces a correct pose and if the scoring function can identify it as a top pose. As a standard or common measure of validation researchers use the root mean squared deviation (RMSD) (Equation 5) which compares the coordinates of the predicted vs. initial conformation of all heavy atoms of both conformations (Dias & de Azevedo Jr., 2008). Overall, RMSD values should be less than 2.0 Å.…”

Section: Validationmentioning

confidence: 99%

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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Molecular Docking Algorithms

Cited by 181 publications

References 1 publication

Molecular Docking and Structure-Based Drug Design Strategies

Molecular Docking and Structure-Based Drug Design Strategies

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

Acoplamiento Molecular: Avances Recientes y Retos

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