Molecular Docking and Structure-Based Drug Design Strategies

Ferreira, Leonardo L. G.; Santos, Ricardo Nascimento dos; Oliva, Glaucius; Andricopulo, Adriano D.

doi:10.3390/molecules200713384

Cited by 1,694 publications

(1,090 citation statements)

References 200 publications

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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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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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“…Docking in combination with scoring function can be used to evaluate large databases for finding out potent drug candidate in silico, which can target the molecule of interest [8].…”

Section: Hit Identificationsmentioning

confidence: 99%

Molecular Docking: Approaches, Types, Applications and Basic Challenges

Dar¹,

Mir²

2017

J Anal Bioanal Tech

152

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Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct. Depending upon binding properties of ligand and target, it predicts the three-dimensional structure of any complex. Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software. Docking simulations predict optimized docked conformer based upon total energy of the system. In spite of all potential approaches, ligand chemistry (tautomerism and ionization), receptor flexibility (single conformation of rigid receptor) and scoring function (differentiate true binding mode) still remained the challenge. Many important aspects of molecular docking in terms of its approaches, types, applications and challenges are briefly discussed in this article.

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“…The flexibility of the target receptor is an essential aspect that must be considered throughout the modelingphase, bearing in mind that substantial conformational change can occur upon ligand binding. [8] …”

Section: Structure -Based Computer Aided Drug Design (Sbdd)mentioning

confidence: 99%

Cadd: Pharmacological Approaches in Drug Design and Drug Discovery

Siju¹

2017

WJPPS

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The objective of drug design is to find a chemical compound that can fit to a specific cavity on a protein target both geometrically and chemically. It is generally recognized that drug discovery and development are time and resources consuming processes. All the world"s major pharmaceutical and biotechnology companies use computational design tools. At their lowest level the contributions represent the replacement of crude mechanical models by displays of structure which are a much more accurate reflection of molecular reality, capable of demonstrating motion and solvent effects. In recent years, the field of computer-aided drug design (CADD) has grown rapidly, enhancing our understanding of complex biological processes and protein-ligand interactions. CADD can predict experimental results with reasonable accuracy and reduced time, cost and equipment.

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Molecular Docking and Structure-Based Drug Design Strategies

Cited by 1,694 publications

References 200 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

Molecular Docking: Approaches, Types, Applications and Basic Challenges

Cadd: Pharmacological Approaches in Drug Design and Drug Discovery

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