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Comparing structural fingerprints using a literature-based similarity benchmark

Noel M. O'Boyle, Roger A. Sayle
2016 Journal of Cheminformatics  
We measure the performance of 28 different fingerprints on the benchmark sets and compare the results to those from the Riniker and Landrum (J Cheminf 5:26, 2013. ) ligand-based virtual screening benchmark  ...  Results: Using this procedure with activity data from ChEMBL, we have created two benchmark datasets for structural similarity that can be used to guide the development of improved measures.  ...  Acknowledgements This work was inspired by a suggestion by Dr. Stefan Senger. We thank the anonymous reviewers for their feedback.  ... 
doi:10.1186/s13321-016-0148-0 pmid:27382417 pmcid:PMC4932683 fatcat:6sxfmxamnngovpiabinp3mewhe

LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds

Faraz Shaikh, Hio Kuan Tai, Nirali Desai, Shirley W. I. Siu
2021 Journal of Cheminformatics  
When testing with our newly compiled compounds from recent literature, we get improved top 10 success rate (66% ours vs. 60% SwissTargetPrediction and 64% SEA) and similar top 1 success rate (45% ours  ...  The performance of LigTMap is comparable to the current best servers SwissTargetPrediction and SEA.  ...  For a query compound, a set of potential targets is selected based on fingerprint similarities to the cocrystallized ligands.  ... 
doi:10.1186/s13321-021-00523-1 pmid:34112240 fatcat:hdaq2s7fb5cctkmonw4xz24r4a

Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing

James Schuler, Ram Samudrala
2019 ACS Omega  
The first version of CANDO implemented a structure-based pipeline that modeled interactions between compounds and proteins on a large scale, generating compound-proteome interaction signatures used to  ...  infer the similarity of drug behavior; the new pipelines accomplish this by incorporating molecular fingerprints and the Tanimoto coefficient.  ...  This work was supported in part by a National Institutes of Health Director's Pioneer Award (DP1OD006779), a National Institutes of Health Clinical and Translational Sciences Award (UL1TR001412), and startup  ... 
doi:10.1021/acsomega.9b02160 pmid:31656912 pmcid:PMC6812124 fatcat:5ztuks7h2rfnhbo6ydi37b6mmy

Benchmarking methods and data sets for ligand enrichment assessment in virtual screening

Jie Xia, Ermias Lemma Tilahun, Terry-Elinor Reid, Liangren Zhang, Xiang Simon Wang
2015 Methods  
Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts.  ...  In addition, we introduced our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structurebased VS approaches, and its implementations to three important  ...  Needless to say, similarity search based on 2D structural fingerprints also plays a pivotal role in LBVS [23] . To date, new approaches are still emerging at a rapid pace.  ... 
doi:10.1016/j.ymeth.2014.11.015 pmid:25481478 pmcid:PMC4278665 fatcat:nuszj6hlrbe53borci42r6dhoq

Screening of antibacterial compounds with novel structure from the FDA approved drugs using machine learning methods

Wen-Xing Li, Xin Tong, Peng-Peng Yang, Yang Zheng, Ji-Hao Liang, Gong-Hua Li, Dahai Liu, Dao-Gang Guan, Shao-Xing Dai
2022 Aging  
Through molecular fingerprint similarity analysis and common substructure analysis, we screened 8 predicted antibacterial small-molecule compounds with novel structures compared with known antibacterial  ...  This study provides a new insight for predicting antibacterial compounds by using approved drugs, the predicted compounds might be used to treat bacterial infections and extend lifespan.  ...  Molecular fingerprints are a way of encoding molecular structure that digitizes the structural information of a compound, which are widely used in drug discovery and virtual screening [15] .  ... 
doi:10.18632/aging.203887 pmid:35150482 pmcid:PMC8876917 fatcat:7yeadvkj7ramlphexdhotkllfq

Mini-fingerprints Detect Similar Activity of Receptor Ligands Previously Recognized Only by Three-Dimensional Pharmacophore-Based Methods

Ling Xue, Florence L. Stahura, Jeffrey W. Godden, Jürgen Bajorath
2001 Journal of chemical information and computer sciences  
Mini-fingerprints (MFPs) are short binary bit string representations of molecular structure and properties, composed of few selected two-dimensional (2D) descriptors and a number of structural keys.  ...  Thus, in these cases, MFPs and pharmacophore fingerprints produce similar results, although they define, in terms of their complexity, opposite ends of the spectrum of methods currently used to study molecular  ...  As a similarity cutoff value, a Tc of 0.85 is often used in the literature, regardless of the particular search tools.  ... 
doi:10.1021/ci000305x pmid:11277728 fatcat:2t2vcabcxvgjdmwzaxs3rmqrvm

jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, Andreas Zell
2011 Journal of Cheminformatics  
against literature methods, comparison of data mining algorithms, similarity searching, and similarity-based data mining.  ...  Additionally, we benchmarked the fingerprint encodings on the large-scale Ames toxicity benchmark using a large-scale linear support vector machine.  ...  Furthermore, the library provides efficient data structures to compare sets of features in the case that the computation of a similarity matrix is required.  ... 
doi:10.1186/1758-2946-3-3 pmid:21219648 pmcid:PMC3033338 fatcat:icxz4cimurf3zcmfuyeprkadgy

Decoys Selection in Benchmarking Datasets: Overview and Perspectives

Manon Réau, Florent Langenfeld, Jean-François Zagury, Nathalie Lagarde, Matthieu Montes
2018 Frontiers in Pharmacology  
on 6 physicochemical properties and select the closest decoys based on (1) a weighted physicochemical similarity and (2) a LADS score based on functional fingerprints similarity elaborated from  ...  Valid active compounds extracted from literature were clustered using chemical fingerprints, and a Tanimoto cut-off of 0.5.  ...  No use, distribution or reproduction is permitted which does not comply with these terms.  ... 
doi:10.3389/fphar.2018.00011 pmid:29416509 pmcid:PMC5787549 fatcat:hiycz5gyf5gpvi2qyvo3hzyn5e

Open-source platform to benchmark fingerprints for ligand-based virtual screening

Sereina Riniker, Gregory A Landrum
2013 Journal of Cheminformatics  
Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening.  ...  Here, we present a standard platform for the benchmarking of 2D fingerprints.  ...  Although 2D fingerprints are simple and based on similarity, they were found to have a significant potential to retrieve structurally diverse molecules.  ... 
doi:10.1186/1758-2946-5-26 pmid:23721588 pmcid:PMC3686626 fatcat:vnzyk3sei5f27hfb4iltx2r32y

Sachem: a chemical cartridge for high-performance substructure search

Miroslav Kratochvíl, Jiří Vondrášek, Jakub Galgonek
2018 Journal of Cheminformatics  
In substructure search, fingerprints are designed to capture important structural aspects of the molecule to aid the decision about whether the molecule contains a given substructure.  ...  the OrChem fingerprint, and the second is a novel method that employs newly designed fingerprints stored in inverted indices.  ...  Availability of data and materials Molecular data used in the benchmarks are publicly available from the PubChem database; exact query sets, datasets and CIDs of the molecules that were randomly selected  ... 
doi:10.1186/s13321-018-0282-y pmid:29797000 pmcid:PMC5966370 fatcat:crjuqymuyfb3jgj6ssoxcmppke

Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis

Jie Xia, Terry-Elinor Reid, Song Wu, Liangren Zhang, Xiang Simon Wang
2018 Journal of Chemical Information and Modeling  
For rational selection of a wide variety of VS approaches, ligand enrichment assessment based on a benchmarking data set has become an indispensable practice.  ...  However, the lack of versatile benchmarking sets for the whole CRs family that are able to unbiasedly evaluate every single approaches including both structure and ligand based VS, somewhat hinders modern  ...  Since the current ligand enrichment assessment applied similarity search based on FCFP_6 fingerprints rather than MACCS structural keys as a LBVS approach.  ... 
doi:10.1021/acs.jcim.8b00004 pmid:29698608 pmcid:PMC6197807 fatcat:mdqt6fklt5egdfobbb6oyz34vm

Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches

Hanna Eckert, Jürgen Bajorath
2007 Drug Discovery Today  
The success of ligand-based virtual-screening calculations is influenced highly by the nature of target-specific structure-activity relationships.  ...  This might pose severe constraints on the ability to recognize diverse structures with similar activity.  ...  Reference molecules and hits were compared using a fingerprint consisting of the publicly available set of 166 MACCS structural keys (MDL Elsevier).  ... 
doi:10.1016/j.drudis.2007.01.011 pmid:17331887 fatcat:cr42wezjjjecthwkguss45drvm

Effective holistic characterization of small molecule effects using heterogeneous biological networks [article]

William Mangione, Zackary Falls, Ram Samudrala
2022 bioRxiv   pre-print
The results indicate there is significant biological information available in the side effect profile of a drug and they can be used to better relate drugs in terms of their therapeutic behavior.  ...  This pipeline highlights the ability of CANDO to accurately relate drugs in a multitarget interactomic context, and paves the way for predicting novel putative drug candidates using the information gleaned  ...  The platform is benchmarked using a protocol that determines how often two drugs indicated for the same disease are considered behaviorally similar based on their proteomic interaction signatures.  ... 
doi:10.1101/2022.03.23.485550 fatcat:4sjpqmdgbrgotjwq2avbloiyhy

Comparative Modeling and Benchmarking Data Sets for Human Histone Deacetylases and Sirtuin Families

Jie Xia, Ermias Lemma Tilahun, Eyob Hailu Kebede, Terry-Elinor Reid, Liangren Zhang, Xiang Simon Wang
2015 Journal of Chemical Information and Modeling  
In DUD-E, the most dissimilar compounds based on ECFP4 fingerprints were chosen as decoys, while DEKOIS 2.0 applied a stricter standard to select structurally divergent decoys, i.e.  ...  These curves and values indicate that MUBD-HDACs data sets are more challenging than the other two benchmarking sets for similarity search using FCFP_6 fingerprint.  ...  DUD-E 45 and DEKOIS 2.0 52 , in terms of ligand enrichment by docking (GOLD) and similarity search based on the function class fingerprints of maximum diameter 6 (FCFP_6) fingerprint.  ... 
doi:10.1021/ci5005515 pmid:25633490 pmcid:PMC4677826 fatcat:tfj3rsugs5eannty6k66f5ruei

Benchmarking Small-Dataset Structure-Activity-Relationship Models for Prediction of Wnt Signaling Inhibition

Mahtab Kokabi, Matthew J. Donnelly, Guangyu Xu
2020 IEEE Access  
Specifically, we examined a total of 72 two-dimensional (2D) QSAR models based on 4 best-performing algorithms, 6 commonly used molecular fingerprints, and 3 typical fingerprint lengths.  ...  We trained these models using a training dataset (56 compounds), benchmarked their performance on 4 figures-of-merit (FOMs), and examined their prediction accuracy using an external validation dataset  ...  MACCS (default length: 256) is a substructure-key based fingerprint using 166 structural keys to characterize SMARTS patterns [39] , [44] .  ... 
doi:10.1109/access.2020.3046190 fatcat:2h7docak5zb3roeertrhjs7rdq
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