scholarly journals Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

2010 ◽  
Vol 50 (12) ◽  
pp. 2079-2093 ◽  
Author(s):  
Vishwesh Venkatraman ◽  
Violeta I. Pérez-Nueno ◽  
Lazaros Mavridis ◽  
David W. Ritchie
2015 ◽  
Vol 13 (03) ◽  
pp. 1541007 ◽  
Author(s):  
Marcus C. K. Ng ◽  
Simon Fong ◽  
Shirley W. I. Siu

Protein–ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden–Fletcher–Goldfarb–Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein–ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51–60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein–ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .


2013 ◽  
Vol 9 (S298) ◽  
pp. 92-97
Author(s):  
Andreas Ritter

AbstractThe advent of large spectroscopic surveys of the Galaxy offers the possibility to compare Galactic models to actual measurements for the first time. I have developed a tool for the comprehensive comparison of any large data set to the predictions made by models of the Galaxy using sophisticated statistical methods, and to visualise the results for any given direction. This enables us to point out systematic differences between the model and the measurements, as well as to identify new (sub-)structures in the Galaxy. These results can then be used to improve the models, which in turn will allow us to find even more substructures like stellar streams, moving groups, or clusters. In this paper I show the potential of this tool by applying it to the RAdial Velocity Experiment (RAVE, Steinmetz 2003) and the Besançon model of the Galaxy Robin et al. 2003.


2015 ◽  
Vol 55 (2) ◽  
pp. 343-353 ◽  
Author(s):  
Martin Lindh ◽  
Fredrik Svensson ◽  
Wesley Schaal ◽  
Jin Zhang ◽  
Christian Sköld ◽  
...  
Keyword(s):  

2010 ◽  
Vol 50 (8) ◽  
pp. 1442-1450 ◽  
Author(s):  
Simon Cross ◽  
Massimo Baroni ◽  
Emanuele Carosati ◽  
Paolo Benedetti ◽  
Sergio Clementi

2020 ◽  
Author(s):  
Samira Norouzi ◽  
Maryam Farahani ◽  
Samad Nejad Ebrahimi

Background: The current outbreak of Coronavirus Disease 2019 (SARS-CoV-2) led to public health emergencies all over the world and made it a global concern. Also, the lack of an effective treatment to combat this virus is another concern that has appeared. Today, increasing knowledge of biological structures like increasing computer power brings about a chance to use computational methods efficiently in different phases of the drug discovery and development for helping solve this new global problem. Methods: In this study, 3D pharmacophores were generated based on thirty-one structures with functional affinity inhibition (antiviral drugs used for SARS and MERS) with IC50<250 µM from the literature data. A 3D-QSAR model has been developed and validated to be utilized in virtual screening. Results: The best pharmacophore models have been utilized as 3D queries for virtual screening to gain promising inhibitors from a data set of thousands of natural compounds retrieved from PubChem. The hit compounds were subsequently used for molecular docking studies to investigate their affinity to the 3D structure of the SARS-CoV-2 receptors. The ADMET properties calculate for the hits with high binding affinity. Conclusion: The study outcomes can help understand the molecular characteristics and mechanisms of the binding of hit compounds to SARS-CoV-2 receptors and promising identification inhibitors that are likely to be evolved into drugs.


SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A167-A168
Author(s):  
Sam Rusk ◽  
Yoav Nygate ◽  
Fred Turkington ◽  
Chris Fernandez ◽  
Nick Glattard ◽  
...  

Abstract Introduction The STOP-Bang is a concise, simple and widely adopted obstructive sleep apnea (OSA) screening tool. However, it has limited predictive ability and is susceptible to subjective reporting bias. Artificial Intelligence (AI) methodologies can be utilized together with existing data in electronic medical records (EMRs) to create new screening tools to increase diagnostic sensitivity and facilitate discovery of preclinical OSA phenotypes. Methods The study comprised two independent retrospective sleep study datasets: 1) Type III HSATS (N=5583) and, 2) Type I polysomnograms (N=1037). Each contained raw sleep study waveforms, manually scored sleep events (respiratory, arousal, sleep staging), and standard report indices (apnea-hypopnea index; AHI, arousal index). Additionally, the first dataset contained 90 EMR based metadata variables and the second dataset contained 54 EMR based metadata variables. Three random forest models were trained to detect OSA diagnostic thresholds (AHI&gt; 5, AHI&gt;15, and AHI&gt;30) over three different screening models: STOP-Bang, P-Bang (blood-pressure, BMI, age, neck-size, gender), and Common Clinical Data Set (CCDS)-OSA (all metadata variables simulating EMR CCDS standard). Results CCDS-OSA ROC-AUC exceeded STOP-Bang and P-Bang for both sleep study collections, resulting in AHI&gt;15 ROC-AUC values of 0.73 and 0.71 (CCDS-OSA) compared to AHI&gt;15 ROC-AUC values of 0.68 and 0.69 (STOP-Bang). Additionally, we analyzed the Gini feature importance ranking of the trained CCDS-OSA model to evaluate which variables showed highest predictive value of OSA. The ranking revealed the top 5 features were the five physiologic based STOP-Bang parameters, followed by EMR based physiologic measurements such as HDL, triglycerides, systolic BP, and disease conditions such as diabetes, hypertension, and depression. Conclusion This study shows that while STOP-Bang contains data critical to OSA screening, a variety of other EMR-based parameters can improve performance of OSA detection. AI-based EMR screening can provide a critical tool for more systematic and accurate screening of undiagnosed sleep apnea. Nationwide standards facilitating patient EMR data interoperable health information exchange, particularly the United States Core Data for Interoperability (USCDI CCDS), holds promise to foster broad clinical and research opportunities. Resulting data sharing will allow application of AI screening tools at the population health scale with ubiquitous, existing EMR data to improve population sleep health. Support (if any):


2007 ◽  
Vol 50 (1) ◽  
pp. 74-82 ◽  
Author(s):  
Paul C. D. Hawkins ◽  
A. Geoffrey Skillman ◽  
Anthony Nicholls

2020 ◽  
Vol 35 ◽  
pp. 153331752092716
Author(s):  
Jin-Hyuck Park

Background: The mobile screening test system for mild cognitive impairment (mSTS-MCI) was developed and validated to address the low sensitivity and specificity of the Montreal Cognitive Assessment (MoCA) widely used clinically. Objective: This study was to evaluate the efficacy machine learning algorithms based on the mSTS-MCI and Korean version of MoCA. Method: In total, 103 healthy individuals and 74 patients with MCI were randomly divided into training and test data sets, respectively. The algorithm using TensorFlow was trained based on the training data set, and then its accuracy was calculated based on the test data set. The cost was calculated via logistic regression in this case. Result: Predictive power of the algorithms was higher than those of the original tests. In particular, the algorithm based on the mSTS-MCI showed the highest positive-predictive value. Conclusion: The machine learning algorithms predicting MCI showed the comparable findings with the conventional screening tools.


ChemInform ◽  
2009 ◽  
Vol 40 (15) ◽  
Author(s):  
Timothy J. Cheeseright ◽  
Mark D. Mackey ◽  
James L. Melville ◽  
Jeremy G. Vinter

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