A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities

Terp, Gitte Elgaard; Johansen, Bent; Christensen, Inge Thøger; Jørgensen, Flemming Steen

doi:10.1021/jm001090l

Cited by 101 publications

(78 citation statements)

References 51 publications

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“…This can be very useful, as it combines the advantages and simultaneously attenuates the shortcomings of each method [64]. Examples of consensus scoring functions are MultiScore, X-Cscore, GFscore, SCS, SeleX-CS and CONSENSUS-DOCK [65][66][67][68][69][70]. Table 2 provides a list of several scoring functions implemented in the most frequently used molecular docking programs.…”

Section: Evaluation Of Binding Energeticsmentioning

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: Evaluation Of Binding Energeticsmentioning

confidence: 99%

Molecular Docking and Structure-Based Drug Design Strategies

et al. 2015

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“…To minimize the impact of this problem and to reduce statistical noise, composite scoring methods have been introduced [89][90][91]. Rather than using a single scoring function, several scoring functions are combined such that in order to be classified as a potential binder, a molecule has to be scored well by a number of different scoring functions.…”

Section: Rescoring -Consensus Scoringmentioning

confidence: 99%

Structure-Based Drug Design: Docking and Scoring

Kroemer

2007

CPPS

281

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This review gives an introduction into ligand -receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major challenges ahead, which are outlined here as well. Approaches to address some of these challenges and the latest developments in the area are presented. Some aspects of the assessment of docking program performance are discussed. A number of successful applications of structure-based virtual screening are described.

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“…The binding free energy is the total of van der Waals interactions, H-bond interactions, electrostatic interactions and the internal static energy of the ligand as shown in Equation 1 [26][27][28][29][30][31][32][33].…”

Section: Dockingmentioning

confidence: 99%

Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme

Ganatra¹

2012

JCSB

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The knowledge of the molecular basis of carcinogenesis has helped to discover new, less toxic chemotherapy agents. At present, considerable attention has been focused on identifying the molecular level interactions of naturally occurring Terpene based substances, capable of inhibiting target enzymes. CDKs enzymes are known as cell regulators in eukaryotic cell cycle. In finding new anti-cancer agents, CDKs are used as target enzymes, particular among them are CDK2 enzymes.Computer based Chem-office and Autodock molecular modeling tools used to understand the ways with which Terpene based natural products interacts with Cyclin-dependent kinase 2 (CDK2). Using in-silico techniques, the binding energy between ligands and receptor enzyme are calculated in the form of ∆G in Kcal.mol -1 . The reported binding energies for series of molecules are ranging from -7.96 to -16.62 Kcal.mol -1 . The negative docking energies and a few hydrogen bonds between ligand and receptor enzyme support the affinity of Terpene based compounds with selected enzyme. Number of hydroxyl groups present in ligand enhances the interaction strength and stability of complex. The finding confirms the affinity of Terpene based natural products as CDK2 inhibitor. Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 EnzymeSunil H Ganatra* and Amita S Suchak Department of Chemistry, Institute of Science, Civil Lines, India Citation: Ganatra SH, Suchak AS (2012) Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme. J Comput Sci Syst Biol 5: 068-073.

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A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities

Cited by 101 publications

References 51 publications

Molecular Docking and Structure-Based Drug Design Strategies

Molecular Docking and Structure-Based Drug Design Strategies

Structure-Based Drug Design: Docking and Scoring

Inhibition Studies of Naturally Occurring Terpene based Compounds with Cyclin-Dependent Kinase 2 Enzyme

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