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One-class approach: models for virtual screening of non-nucleoside HIV-1 reverse transcriptase inhibitors based on the concept of continuous molecular fields

P. V. Karpov, I. I. Baskin, N. I. Zhokhova, M. B. Nawrozkij, A. N. Zefirov, A. S. Yablokov, I. A. Novakov, N. S. Zefirov
2011 Russian chemical bulletin  
The representation of molecular structures of organic ligands based on continuous molecular fields can be used to build classification models of higher quality com pared to conventional approaches using  ...  The training set included 786 structures of 2 substituted pyrimidino nes and their inhibitory activity against the enzyme of wild type and mutant (К103, IRLL98, Y188L) HIV 1 strains.  ...  Most of compounds from the set under study have the molecular similarity with the decoys of about ≤0.75, which characterizes this data set as a diverse one.  ... 
doi:10.1007/s11172-011-0372-8 fatcat:jsx4c4qi5fgy7djnsnojy3s2fu

Database fingerprint (DFP): an approach to represent molecular databases

Eli Fernández-de Gortari, César R. García-Jacas, Karina Martinez-Mayorga, José L. Medina-Franco
2017 Journal of Cheminformatics  
A major future goal is to apply the DFP for virtual screening and developing DFP for other data sets based on several different type of fingerprints.  ...  Molecular fingerprints are widely used in several areas of chemoinformatics including diversity analysis and similarity searching.  ...  This paper is dedicated to the memory of Juan Antonio Fernández Díaz Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13321-017-0195-1 pmid:28224019 pmcid:PMC5293704 fatcat:upcwszhikzcndfy32hz4ylp23i

Feature optimization in high dimensional chemical space: statistical and data mining solutions

Jinuraj K. R., Rakhila M., Dhanalakshmi M., Sajeev R., Akshata Gad, Jayan K., Muhammed Iqbal P., Andrew Titus Manuel, Abdul Jaleel U. C.
2018 BMC Research Notes  
It was also shown that similarities in the activity of compounds were due to the molecular descriptors which were not apparent in prima facie structural studies.  ...  Objectives: The primary goal of this experiment is to prioritize molecular descriptors that control the activity of active molecules that could reduce the dimensionality produced during the virtual screening  ...  Acknowledgements The authors are grateful to the support given by the Centre for Cheminformatics, Department of Chemistry, Malabar Christian College, Calicut; CSIR-OSDD Research Unit, IISc Campus, Bangalore  ... 
doi:10.1186/s13104-018-3535-y pmid:30001749 pmcid:PMC6044099 fatcat:ngeb3q6t7va4rmsgwy55fsherq

The Use of MoStBioDat for Rapid Screening of Molecular Diversity

Andrzej Bak, Jaroslaw Polanski, Agata Kurczyk
2009 Molecules  
The substructure bias, assessing the level of molecular similarity, is accomplished by setting the similarity measure ranging from 0.1 to 1.0.  ...  The substructure bias, assessing the level of molecular similarity, is accomplished by setting the similarity measure ranging from 0.1 to 1.0.  ... 
doi:10.3390/molecules14093436 pmid:19783936 pmcid:PMC6254917 fatcat:ih25nge46nau7nqxfyycuz5u5m

A Quantum-Based Similarity Method in Virtual Screening

Mohammed Al-Dabbagh, Naomie Salim, Mubarak Himmat, Ali Ahmed, Faisal Saeed
2015 Molecules  
The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints.  ...  One of the most widely-used techniques for ligand-based virtual screening is similarity searching.  ...  The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints.  ... 
doi:10.3390/molecules201018107 pmid:26445039 fatcat:urt6xjonczbxhlgg6n3eatvz2u

Cheminformatics analysis and learning in a data pipelining environment

Moises Hassan, Robert D. Brown, Shikha Varma-O'Brien, David Rogers
2006 Molecular diversity  
In this paper we review SciTegic's methodology for molecular fingerprints, molecular similarity, molecular clustering, maximal common subgraph search and Bayesian learning.  ...  Case studies are described showing the application of these methods to the analysis of discovery data such as chemical series and high throughput screening results.  ...  Acknowledgements The authors would like to acknowledge Mathew Hahn for early work on many of the components that made this work possible, and for the time to write this paper.  ... 
doi:10.1007/s11030-006-9041-5 pmid:17031533 fatcat:ej5yepomobb3dfkxe64plr2xey

Chemoinformatic Approaches for Inhibitors of DNA Methyltransferases: Comprehensive Characterization of Screening Libraries

Jakyung Yoo, José Luis Medina-Franco
2011 Computational Molecular Bioscience  
The compound databases were assessed in terms of physicochemical properties, molecular scaffolds, and fingerprints.  ...  Overall, the analysis of the distribution of physicochemical properties indicates that the DNMT focused library and the two natural products collections have molecules with properties similar to approved  ...  Similarity is colored using a continuous color scale from red (high similarity) to green (low similarity). Figure 4 . 4 CSR curves for representative data sets.  ... 
doi:10.4236/cmb.2011.11002 fatcat:4rb67kpx3vg4nhltb7ya6wmhvq

Towards the Bioassay Activity Landscape Modeling in Compound Databases

José Luis Medina-Franco, Jacob Waddell
2017 Journal of the Mexican Chemical Society  
This strategy is general and can be applied to any data set screened across multiple bioassays.  ...  We also present a visual representation of the chemical space of an in-house data set using a recently developed web-based public tool.  ...  This work was supported by the State of Florida Executive Office of the Governor's Office of Tourism, Trade, and Economic Development.  ... 
doi:10.29356/jmcs.v56i2.316 fatcat:63dckyhfhfhs3ezf3ukzeeoxyy

HHVSF: A Framework to Accelerate Drug-Based High-Throughput Virtual Screening on High-Performance Computers [chapter]

Pin Chen, Xin Yan, Jiahui Li, Yunfei Du, Jun Xu
2018 Lecture Notes in Computer Science  
Among the most popular molecular docking and molecular structure similarity packages, Autodock_vina (ADV) and WEGA were chosen to carry out experiments.  ...  For WEGA, 958 million conformations were screened and analyzed in 34.12 min with 4000 cores, of which throughput reached up to 9448 molecules per second, 6430 molecules per second on average.  ...  This work was performed by the auspices of the NSFC (U1611261), GD Frontier & Key Techn, Innovation Program (2015B010109004).  ... 
doi:10.1007/978-3-319-69953-0_1 fatcat:kgopacnqbrf4fhi2mcu6rlbv4u

Ligandbased Virtual screening using Fuzzy Correlation Coefficient

Ali Ahmed, Ammar Abdo, Naomie Salim
2011 International Journal of Computer Applications  
Selection and identification of a subset of compounds from libraries or databases, which are likely to possess a desired biological activity is the main target of ligand-based virtual screening approaches  ...  The main challenge of such approaches is achieving of high recall of active molecules. In this paper we presented fuzzy correlation coefficients (FCC), which is used as a similarity coefficient.  ...  For screening experiments, three data sets (DS1-DS3) were chosen [17] from MDDR data base.  ... 
doi:10.5120/2386-3158 fatcat:wvhbsra3rjbqjlmbm4aq3a2wkq

Ligand-Based Virtual Screening using Random Walk Kernel and Empirical Filters

M.P. Preeja, Hemant Palivela, K.P. Soman, Prashant S. Kharkar
2015 Procedia Computer Science  
Molecular graphs are very expressive which allow faster implementation of the machine-learning algorithms.  ...  The data generated during various stages of the drug discovery is drastically increasing and it forces machine-learning scientist to implement more effective and fast methods for the utilization of data  ...  Accuracy of the method was tested with PTC and MUTAG data sets. The PTC data set contains a set of 344 compounds classified according to their carcinogenicity [12] .  ... 
doi:10.1016/j.procs.2015.07.508 fatcat:4bzda3wow5b3teznkzhmd2ddsm

Development and Testing of Druglike Screening Libraries

Junmei Wang, Yubin Ge, Xiang-Qun Xie
2018 Journal of Chemical Information and Modeling  
Then we compiled a set of screening libraries from about 20 million druglike ZINC molecules by running fingerprint-based similarity searches against known drug molecules.  ...  For example, with the Tanimoto coefficient being set to 0.75, 36% of external actives were retrieved and the enrichment factor was 13.  ...  The developed screening libraries were assessed by a set of test data sets of bioactives.  ... 
doi:10.1021/acs.jcim.8b00537 pmid:30563329 pmcid:PMC6756465 fatcat:hycwdveku5c7lko4xl72inrtxe

Ligand-Based Virtual Screening Using Graph Edit Distance as Molecular Similarity Measure

Carlos Garcia-Hernandez, Alberto Fernández, Francesc Serratosa
2019 Journal of Chemical Information and Modeling  
This is exemplified with six publicly available data sets: DUD-E, MUV, GLL&GDD, CAPST, NRLiSt BDB, and ULS-UDS.  ...  for ligand-based virtual screening applications, which estimate the bioactivity of a chemical on the basis of the bioactivity of similar compounds.  ...  in the context of LBVS, and the measure of molecular similarity used is an important feature that determines the success or not of a virtual screening method.  ... 
doi:10.1021/acs.jcim.8b00820 pmid:30920214 pmcid:PMC6668628 fatcat:tnf7vhbljbef3egxshz6vjogze

Design of a High Fragment Efficiency Library by Molecular Graph Theory

Jennifer Venhorst, Sara Núñez, Chris G. Kruse
2010 ACS Medicinal Chemistry Letters  
The data graph collection of Discngine as implemented in PipelinePilot was applied to perform the graph pharmacophore similarity matching between the reference and the GDB-13 data sets, leading to the  ...  Molecular graph theory was used to design a unique and diverse, high-efficiency fragment screening collection.  ...  ACKNOWLEDGMENT We acknowledge the help of Dr. Antoniou and Dr. McCormack for proofreading the manuscript, Dr. Bronger for assistance with the chemical tractability of the fragments, and Dr.  ... 
doi:10.1021/ml100163s pmid:24900238 pmcid:PMC4007847 fatcat:nln5agplfrdldlg2gf53vjsfym

MolDIA: XML based system of molecular diversity analysis towards virtual screening and QSPR†

A. G. Maldonado, M. Petitjean, J.-P. Doucet, A. Panaye, B. T. Fan
2006 SAR and QSAR in environmental research (Print)  
Screening and data-mining techniques improve the analysis, retrieval and management of big quantity of data.  ...  In Virtual Screening, the data available (e.g. molecular structures, physicochemical properties, etc.) is processed to build models that allow the treatment of these data.  ... 
doi:10.1080/10659360600562038 pmid:16513549 fatcat:7ocstvh53ng55bn72rvuxpaq2e
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