QUASI:  A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity

2007 ◽  
Vol 47 (3) ◽  
pp. 1007-1020 ◽  
Author(s):  
Nikolay P. Todorov ◽  
Ian L. Alberts ◽  
Iwan J. P. de Esch ◽  
Philip M. Dean
Keyword(s):  
Virtual Screening ◽  
Partial Similarity ◽  
Novel Method ◽  
Flexible Ligands

QUASI: A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity.

ChemInform ◽  
2007 ◽  
Vol 38 (33) ◽  
Author(s):  
Nikolay P. Todorov ◽  
Ian L. Alberts ◽  
Iwan J. P. de Esch ◽  
Philip M. Dean
Keyword(s):  
Virtual Screening ◽  
Partial Similarity ◽  
Novel Method ◽  
Flexible Ligands

scholarly journals Prospective Assessment of Virtual Screening Heuristics Derived Using a Novel Fusion Score

2017 ◽  
Vol 22 (8) ◽  
pp. 995-1006 ◽  
Author(s):  
Dante A. Pertusi ◽  
Gregory O’Donnell ◽  
Michelle F. Homsher ◽  
Kelli Solly ◽  
Amita Patel ◽  
...  
Keyword(s):  
Machine Learning ◽  
Virtual Screening ◽  
High Throughput Screening ◽  
Screening Methods ◽  
Active Compounds ◽  
Active Chemical ◽  
Prospective Assessment ◽  
Novel Method ◽  
Early Drug ◽  
Chemical Matter

High-throughput screening (HTS) is a widespread method in early drug discovery for identifying promising chemical matter that modulates a target or phenotype of interest. Because HTS campaigns involve screening millions of compounds, it is often desirable to initiate screening with a subset of the full collection. Subsequently, virtual screening methods prioritize likely active compounds in the remaining collection in an iterative process. With this approach, orthogonal virtual screening methods are often applied, necessitating the prioritization of hits from different approaches. Here, we introduce a novel method of fusing these prioritizations and benchmark it prospectively on 17 screening campaigns using virtual screening methods in three descriptor spaces. We found that the fusion approach retrieves 15% to 65% more active chemical series than any single machine-learning method and that appropriately weighting contributions of similarity and machine-learning scoring techniques can increase enrichment by 1% to 19%. We also use fusion scoring to evaluate the tradeoff between screening more chemical matter initially in lieu of replicate samples to prevent false-positives and find that the former option leads to the retrieval of more active chemical series. These results represent guidelines that can increase the rate of identification of promising active compounds in future iterative screens.

scholarly journals Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening

2019 ◽  
Vol 9 (21) ◽  
pp. 4538 ◽  
Author(s):  
Tatiana F. Vieira ◽  
Sérgio F. Sousa
Keyword(s):  
Virtual Screening ◽  
Open Source ◽  
Ligand Docking ◽  
Protein Targets ◽  
Starting Point ◽  
First Choice ◽  
Docking Program ◽  
Binding Pockets ◽  
Overall Performance ◽  
Flexible Ligands

AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting point for many virtual screening campaigns, particularly in academia. Here, we evaluated the performance of AutoDock and Vina against an unbiased dataset containing 102 protein targets, 22,432 active compounds and 1,380,513 decoy molecules. In general, the results showed that the overall performance of Vina and AutoDock was comparable in discriminating between actives and decoys. However, the results varied significantly with the type of target. AutoDock was better in discriminating ligands and decoys in more hydrophobic, poorly polar and poorly charged pockets, while Vina tended to give better results for polar and charged binding pockets. For the type of ligand, the tendency was the same for both Vina and AutoDock. Bigger and more flexible ligands still presented a bigger challenge for these docking programs. A set of guidelines was formulated, based on the strengths and weaknesses of both docking program and their limits of validation.

The removal and morphology of intact biofilms from implanted venous access devices

1995 ◽  
Vol 53 ◽  
pp. 1020-1021
Author(s):  
M.A. Gregory ◽  
G.P. Hadley
Keyword(s):  
Patient Selection ◽  
Surgical Oncology ◽  
Venous Access ◽  
Common Procedure ◽  
Indwelling Catheters ◽  
Careful Patient ◽  
Novel Method ◽  
The Subject ◽  
Vascular Catheters ◽  
Venous Access Devices

The insertion of implanted venous access systems for children undergoing prolonged courses of chemotherapy has become a common procedure in pediatric surgical oncology. While not permanently implanted, the devices are expected to remain functional until cure of the primary disease is assured. Despite careful patient selection and standardised insertion and access techniques, some devices fail. The most commonly encountered problems are colonisation of the device with bacteria and catheter occlusion. Both of these difficulties relate to the development of a biofilm within the port and catheter. The morphology and evolution of biofilms in indwelling vascular catheters is the subject of ongoing investigation. To date, however, such investigations have been confined to the examination of fragments of biofilm scraped or sonicated from sections of catheter. This report describes a novel method for the extraction of intact biofilms from indwelling catheters.15 children with Wilm’s tumour and who had received venous implants were studied. Catheters were removed because of infection (n=6) or electively at the end of chemotherapy.

Longitudinal Changes in Individual BrainAGE in Healthy Aging, Mild Cognitive Impairment, and Alzheimer’s Disease

GeroPsych ◽  
2012 ◽  
Vol 25 (4) ◽  
pp. 235-245 ◽  
Author(s):  
Katja Franke ◽  
Christian Gaser
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Healthy Aging ◽  
Brain Aging ◽  
Elderly Subjects ◽  
Additional Increase ◽  
Longitudinal Changes ◽  
Novel Method ◽  
The Brain

We recently proposed a novel method that aggregates the multidimensional aging pattern across the brain to a single value. This method proved to provide stable and reliable estimates of brain aging – even across different scanners. While investigating longitudinal changes in BrainAGE in about 400 elderly subjects, we discovered that patients with Alzheimer’s disease and subjects who had converted to AD within 3 years showed accelerated brain atrophy by +6 years at baseline. An additional increase in BrainAGE accumulated to a score of about +9 years during follow-up. Accelerated brain aging was related to prospective cognitive decline and disease severity. In conclusion, the BrainAGE framework indicates discrepancies in brain aging and could thus serve as an indicator for cognitive functioning in the future.

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