Protein‐Ligand Docking

Morris, Garrett M.; Olson, Arthur J.; Goodsell, David S.

doi:10.1002/9783527613168.ch3

Cited by 24 publications

(16 citation statements)

References 53 publications

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“…The fitness function is based on estimations of the binding energy between the peptide ligand and the target protein. In order to estimate the binding energy, we have used a molecular mechanics approach known as docking [34]. Our calculations rely on Autodock 3.0.5 [33].…”

Section: An Evolutionary Approach To Peptide Designmentioning

confidence: 99%

Evolutionary algorithms and de novo peptide design

2005

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One of the goals of computational chemistry is the automated de novo design of bioactive molecules. Despite significant progress in computational approaches to ligand design and efficient evaluation of binding energy, novel procedures for ligand design are required. Evolutionary computation provides a new approach to this design issue. This paper presents an automated methodology for computer-aided peptide design based on evolutionary algorithms. It provides an automatic tool for peptide de novo design, based on protein surface patches defined by user. Regarding the restrictive constrains of this problem a special emphasis has been made on the design of the evolutionary algorithms implemented.

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Section: An Evolutionary Approach To Peptide Designmentioning

confidence: 99%

Evolutionary algorithms and de novo peptide design

2005

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“…Optimistically the results from this study will provide insight about the design of effective antiviral drugs against dengue virus which will prove to be a valuable resource for further research. Different softwares such as ChemBioDraw ® Ultra 13.0 [34], HyperChem professional 8.0.10 [35], AutoDock [14], LigandScout [15] and VMD [16] were selected and used to get the results. The complete drug designing scheme has been demonstrated in Figure 2.…”

Section: Introductionmentioning

confidence: 99%

In Silico Molecular Docking Studies and Design of Dengue Virus Inhibitors

Ruba¹,

Arooj²,

Naz³

2014

IOSRJPBS

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“…This process can be a very challenging problem given the degree of conformational flexibility at the ligand-macromolecular level [39][40][41][42][43][44]. Docking consists of two parts, namely, (i) prediction of the conformation, orientation and position (pose) of the bioactive compound into the binding pocket, and (ii) estimation of the tightness of target-ligand interactions (scoring) to guide conformational sampling [45].…”

Section: Introductionmentioning

confidence: 99%