Ligand-based Screening and Selection
An enhancement of bayesian inference network for ligand-based virtual screening using features selection
... BIN model based on feature selection: This model of BIN is based on using subset of molecule’s features. To achieve this objective, two steps were used. First, we prepare training data that consists ...
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Fragment reweighting in ligand-based virtual screening
... searching. Ligand-based virtual screening based on sub-fragments is also reviewed in this ...feature selection algorithm to select the important fragments, or using the idea of ...
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Evaluation of machine-learning methods for ligand-based virtual screening
... three selection methods were again used for this purpose; in each case, a total of 200 inactive molecules was selected from the MDDR database that did not belong to the activity class under ...third ...
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Application and Development of Computational Methods for Ligand-Based Virtual Screening
... feature selection methods to identify fingerprint features that were responsible for the recall of different com- pound ...feature selection, compare the search performance of unmodified and reduced ...
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Evaluation of machine-learning methods for ligand-based virtual screening
... random selection of molecules for biological screening would have identified just 1% of the ...virtual screening purposes when sets of non-binary descriptors are available to characterise the ...
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Ligand-based virtual screening using binary kernel discrimination
... technique based on atom environment fingerprints, information-gain-based feature selection, and a naïve Bayesian classifier ...[8]. Based on these comparisons (and on comparisons with two ...
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Condorcet and borda count fusion method for ligand-based virtual screening
... Virtual screening, Similarity coefficients, Data fusion Background Virtual screening refers to the use of a computer-based method to process compounds from a library or data- base of compounds in ...
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Contact-based ligand-clustering approach for the identification of active compounds in virtual screening
... contact selection were ...contact selection was made as a control for the presence of the specific contacts that were not included in other ...Atom selection by partial charge was used for selections ...
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Discovery of a novel IKK-β inhibitor by ligand-based virtual screening techniques
... similarity screening, the query molecules were ranked using the combo ...virtually screening the ensemble of conformations for each reference molecule against all single query molecule ...
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Ligand efficiency as a guide in fragment hit selection and optimization
... A common approach for hit identification is high-throughput screening (HTS) [ 1 ]. In HTS a large number of compounds (10 6 ) are screened to assess biological activity against a target. Nevertheless, considering ...
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4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening
... GMM based on a predefined number of Gaussian com- ...model selection step that determines an optimal number of components is neces- ...model selection criter- ions, such as the Bayesian information ...
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In Silico Structure-Based Screening of Large Ligand Library Against Virulence Factors of Drug Resistant Pathogens
... determine any bacterial growth, as indicated by cloudiness of the solution or growth of cells at the bottom of the wells. Virulence Assay on Validated List of EsxA Hit Compounds Given that EsxA is a virulence factor of ...
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Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening
... for ligand affinity, 22 is the sum over all pairs of ligand and target protein atoms within a specified cutoff ...energetic selection of compounds that includes a VDW attractive contribution, or ...
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Consensus queries in ligand-based virtual screening experiments
... In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein ...than screening using a ...
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Fusing similarity rankings in ligand-based virtual screening.
... of the ranking after the database had been ranked in order of decreasing similarity with the reference structure). This procedure was repeated for each of the other 24 similarity measures, so that it was possible to ...
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New similarity measures for ligand-based virtual screening
... Zoete et al., 2009) , and many types of research are focused on it. The molecules databases (fingerprint) contain a large number of bit-strings that represent the molecules features (Bajorath, 2017; from Structure, 1997; ...
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A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening
... and ligand-based in silico screening methods can be ...target screening (MSM-MTS) method was adopted as a structure-based screening method, and the machine-learning docking score ...
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Evaluation of a Bayesian inference network for ligand-based virtual screening
... virtual screening approaches that can be used in any particular circumstances depend principally upon the amounts and types of data that are available [2-7]; here we focus on ligand-based approaches, ...
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Ligand-based virtual screening interface between PyMOL and LiSiCA
... reference ligand and the target database, defining all of the LiSiCA’s options, loading previously completed projects and outputting a list of the highest scoring mole- cules that can be visualized in the PyMOL ...
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Evaluation of a Bayesian inference network for ligand-based virtual screening
... virtual screening approaches that can be used in any particular circumstances depend principally upon the amounts and types of data that are available [2-7]; here we focus on ligand-based approaches, ...
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