scholarly journals Extra Precision Glide:  Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

2006 ◽  
Vol 49 (21) ◽  
pp. 6177-6196 ◽  
Author(s):  
Richard A. Friesner ◽  
Robert B. Murphy ◽  
Matthew P. Repasky ◽  
Leah L. Frye ◽  
Jeremy R. Greenwood ◽  
...  
Keyword(s):  
Glide Docking ◽  
Docking And Scoring

Prediction of Protein−Ligand Interactions. Docking and Scoring:  Successes and Gaps

2006 ◽  
Vol 49 (20) ◽  
pp. 5851-5855 ◽  
Author(s):  
Andrew R. Leach ◽  
Brian K. Shoichet ◽  
Catherine E. Peishoff
Keyword(s):  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Docking And Scoring

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

2009 ◽  
Vol 23 (8) ◽  
pp. 527-539 ◽  
Author(s):  
Sameer Kawatkar ◽  
Hongming Wang ◽  
Ryszard Czerminski ◽  
Diane Joseph-McCarthy
Keyword(s):  
Fragment Screening ◽  
Docking And Scoring

scholarly journals Natural products as inhibitors of COVID-19 main protease – A virtual screening by molecular docking

2020 ◽  
Author(s):  
Marzieh omrani ◽  
Mohammad Bayati ◽  
Parvaneh Mehrbod ◽  
Samad Nejad-Ebrahimi
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
High Throughput ◽  
Herbal Medicines ◽  
Respiratory Illness ◽  
Fast Method ◽  
Main Protease ◽  
Glide Docking ◽  
Adme Properties ◽  
High Throughput Virtual Screening

Abstract Background: The novel coronavirus (2019-nCoV) causes a severe respiratory illness that was unknown in the human before. Its alarmingly quick transmission to many countries across the world resulted in a worldwide health emergency. It has caused a notable percentage of morbidity and mortality. Therefore, an imminent need for drugs to combat this disease has been increased. Global collaborative efforts from scientists are underway to find a therapy to treat infections and reduce death cases. Herbal medicines and purified natural products have been reported to have antiviral activity against Coronaviruses (CoVs).Methods: In this study, a High Throughput Virtual Screening (HTVS) protocol was used as a fast method on the discovery of novel drug candidates as the COVID-19 main protease inhibitors. Over 180,000 natural product-based compounds were obtained from the ZINC database and virtually screened against the COVID-19 main protease. In this study, the Glide docking program was applied for high throughput virtual screening. Extra precision (XP) and in a combination of Prime module, induced-fit docking (IFD) approach was also used. Additionally, the ADME properties of all compounds were analyzed, and the final selection was carried out based on the Lipinski rule of five. Results: The nineteen compounds were selected and introduced as new potential inhibitors. The compound ZINC08765174 (1-[3-(1H-indol-3-yl) propanoyl]-N-(4-phenylbutan-2-yl)piperidine-3-carboxamide) showed a strong binding affinity (-11.5 kcal/mol) to the crucial residues of COVID-19 main protease comparing to peramivir (-9.8 kcal/mol) as a positive control.Conclusions: The excellent ADME properties proposed the opportunity of this compound to be a promising candidate for the treatment of COVID-19.

Docking and scoring protein complexes: CAPRI 3rd Edition

2007 ◽  
Vol 69 (4) ◽  
pp. 704-718 ◽  
Author(s):  
Marc F. Lensink ◽  
Raúl Méndez ◽  
Shoshana J. Wodak
Keyword(s):  
Protein Complexes ◽  
Docking And Scoring

Discovery of novel anaplastic lymphoma kinase inhibitors: Structure and energy-based pharmacophore strategy

2019 ◽  
Vol 18 (03) ◽  
pp. 1950014 ◽  
Author(s):  
Nivya James ◽  
V. Shanthi ◽  
K. Ramanathan
Keyword(s):  
Lung Cancer ◽  
Anaplastic Lymphoma Kinase ◽  
Density Functional ◽  
Kinase Inhibitors ◽  
Chemical Reactivity ◽  
Pharmacophore Model ◽  
Density Functional Theory Calculations ◽  
Alk Inhibitors ◽  
Anaplastic Lymphoma ◽  
Glide Docking

The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), which were then subjected to molecular docking and ADME prediction. These approaches resulted in the identification of five hits, namely, nebivolol, HDY, D42, 796, and LZE having higher Glide docking scores and promising ADME properties with augmented CNS involvement. Moreover, molecular dynamics simulations were performed to validate the inhibitory activity of the hit compounds, and density functional theory calculations were carried out to scrutinize the chemical reactivity of the hits. Subsequent interaction and scaffold analysis identified prominent interactions of the hits with ALK kinase domain and scaffolds with anti-tumor activity against lung cancer cell lines. We strongly believe that the study provides an outlook for the sighting of novel and potent ALK inhibitors in the near future.

Docking and scoring with alternative side-chain conformations

2009 ◽  
Vol 74 (3) ◽  
pp. 712-726 ◽  
Author(s):  
Christoph Hartmann ◽  
Iris Antes ◽  
Thomas Lengauer
Keyword(s):  
Side Chain ◽  
Docking And Scoring ◽  
Chain Conformations

Docking and Scoring

2007 ◽  
pp. 255-281
Author(s):  
P.F.W. Stouten ◽  
R.T. Kroemer
Keyword(s):  
Docking And Scoring
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