Recent Advances in Docking and Scoring

Krovat, Eva M.; Steindl, Theodora M.; Langer, Thierry

doi:10.2174/1573409052952314

Cited by 169 publications

(123 citation statements)

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“…This procedure decreases the average energy of the chromosome ensemble by transmitting favorable structural characteristics from one population to another, reducing therefore, the conformational space to be explored. The GA routine is recursively executed and, after a reasonable number of conformational search-and-evaluation cycles, converges to a conformation (chromosome) corresponding to the global energy minimum [36].…”

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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“…However, it needs to be reiterated that even the most sophisticated methods of free energy estimation are not wholly accurate. In the absence of a single function that is valid for many or all targets [150], a strategy of merging several diverse scoring functions to form a consensus has emerged. This was proposed by Charifson [151] because the combination of diverse functions could potentially compensate for the weaknesses of individual functions, and thus yield better overall scoring.…”

Section: Consensus Scoringmentioning

confidence: 99%

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

Spyrakis

Cozzini

Kellogg

2016

Nuclear Receptor Research

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Abstract. During the last decade, computational methods, which were for the most part developed to study protein-ligand interactions and especially to discover, design and develop drugs by and for medicinal chemists, have been successfully applied in a variety of food science applications [1,2]. It is now clear, in fact, that drugs and nutritional molecules behave in the same way when binding to a macromolecular target or receptor, and that many of the approaches used so extensively in medicinal chemistry can be easily transferred to the fields of food science. For instance, nuclear receptors are common targets for a number of drug molecules and could be, in the same way, affected by the interaction with food or food-like molecules. Thus, key computational medicinal chemistry methods like molecular dynamics can be used to decipher protein flexibility and to obtain stable models for docking and scoring in food-related studies, and virtual screening is increasingly being applied to identify molecules with potential to act as endocrine disruptors, food mycotoxins, and new nutraceuticals [3][4][5]. All of these methods and simulations are based on protein-ligand interaction phenomena, and represent the basis for any subsequent modification of the targeted receptor's or enzyme's physiological activity. We describe here the energetics of binding of biological complexes, providing a survey of the most common and successful algorithms used in evaluating these energetics, and we report case studies in which computational techniques have been applied to food science issues. In particular, we explore a handful of studies involving the estrogen receptors for which we have a long-term interest.

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“…A large variety of different approaches for a solution of this problem has been applied [6,8,162,163,164,165] ranging from fragment-based (e.g., DOCK [166,169], FlexX [6,8,11,170], SLIDE [171], SURFLEX [172], and GLIDE [173,174,175]) over stochastic optimization methods for finding the global minimum (e.g., GOLD [176,177,178], AutoDock [179,180], PLANTS [181,182,183], ICM [184], QXP [185], and PRO_LEADS [186,187]) to multiconformer docking (e.g., FRED [188]). …”

Section: Influence Of Ph and Protonation States In Docking Studiesmentioning

confidence: 99%

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

Yunta¹

2014

AJMO

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Protonation states are sometimes crucial for free energy calculations to predict binding ability of molecules to receptors, a main subject for drug design. This mini-review seeks to identify the importance of knowing the influence of pH in such studies to better achieve correct predictions for drug candidates. Protonation states, for both proteins and drugs, need to be considered in docking studies although they have been usually neglected.

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Recent Advances in Docking and Scoring

Cited by 169 publications

References 0 publications

Molecular Docking and Structure-Based Drug Design Strategies

Molecular Docking and Structure-Based Drug Design Strategies

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

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