Probabilistic Approaches in Activity Prediction

Filimonov, Dmitry; Poroikov, Vladimir

doi:10.1039/9781847558879-00182

Cited by 86 publications

(53 citation statements)

References 99 publications

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“…C помощью процедуры скользящего контроля с исключением по одному, рассчитывалась инвариантная точность прогноза (IAP) [9], которая совпадает по величине со значением площади под кривой (AUC), вычисляемой при ROC-анализе.…”

Section: прогноз и валидацияunclassified

“…Этот способ описания успешно используется при прогнозе биологической активности низкомолекулярных химических соединений на протяжении ряда лет. При этом оценка принадлежности вещества к тому или иному виду биологической активности производится с помощью алгоритма PASS [9][10][11]. Одна из главных областей применения этой методики -поиск лигандов, специфичных к различным белкам-мишеням, что близко по смыслу к распознаванию пептидов, связываемых модифицирующим ферментом.…”

Section: Introductionunclassified

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Application of molecular descriptors for recognition of phosphorylation sites in amino acid sequences

et al. 2017

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Recognition of the phosphorylation sites in proteins is required for reconstruction of regulatory processes in living systems. This task is complicated because the phosphorylation motifs in amino acid sequences are considerably degenerated. To improve the prediction efficacy researchers often use additional descriptors, which should reflect physicochemical features of site-surrounding regions. We have evaluated the reasonability of this approach by applying molecular descriptors (MNA) for structural presentation of the peptide segments. Comparative testing was performed using the prognostic method PASS and two input data types: sets of the MNA descriptors represented peptides as chemical structures and amino acid sequences written using a one-letter code. Training sets were classified in accordance with the established types of the enzymes (protein kinases), modifying corresponding phosphorylation sites. The accuracy estimates obtained by prognosis validation for various classes of substrates were significantly different with both the letters and molecular descriptors. In case of the letter description, the prognosis accuracy demonstrated less dependence on the length of peptides in the training set, while in the case of structural descriptors the accuracy level was determined by the peptide size and descriptor characteristics (MNA levels). The maximal prognosis accuracy related to various kinase families was achieved at different sizes of molecular fragments covered by the MNA descriptors of corresponding levels. This obviously reflected structural differences in surroundings of phosphorylation sites modified by various protein kinases. The use of molecular descriptors provided the prognostic results comparable with the results obtained using traditional letter representation. The prognosis accuracy demonstrated less dependence on the method describing site-surrounding peptides at higher accuracy rates. Applying the MNA descriptors it is possible to achieve better accuracy in the cases when the letter description cannot provide acceptable accuracy.

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Section: прогноз и валидацияunclassified

Section: Introductionunclassified

Application of molecular descriptors for recognition of phosphorylation sites in amino acid sequences

et al. 2017

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“…48 Regarding anti-infective activities, only antihelmintic activity (Pa > 0.6) of studied thioxanthones were predicted by PASS in accordance with reported experimental observations ( Tables 3 and 4). 49 According to PASS predictions the most plausible human biological targets of hydroxylated xanthones are oxidoreductases, particularly CYP450 isoforms (Pa > 0.9), similar to other planar polyphenols such as quercetin. Other targets pointed out by program PASS may be involved in glucose and lipids metabolism and homeostasis,e.g.…”

Section: In Silico Analysismentioning

confidence: 99%

An efficient and convenient microwave-assisted chemical synthesis of (thio)xanthones with additional in vitro and in silico characterization

Verbanac

Jain

et al. 2012

Bioorganic & Medicinal Chemistry

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“…The predicted activity spectrum is presented in PASS by the list of activities with the probabilities 'to be active' (Pa) calculated for each activity. [28][29][30]32] The probability, Pa, reflects the similarity of a molecule under prediction with the structures of molecules, which are the most typical in a sub-set of 'actives' in the structure-activity relationship (SAR) PASS database. According to the PASS output the synthetized compounds could potentially act as omptin inhibitors (Pa ≥ 0.5).…”

Section: In Silico Analysis Antibacterial Activity and Structure Actmentioning

confidence: 99%

“…Bacterial strains used as the primary screening panel included two strains of Gram-negative species, Esherichia coli (TolC-) (efflux pump deficient strain ECM1556 tolC:Tn10) [27] In Silico Predictions of plausible biological targets and pharmacological activities were made by web-service PASS (http://www.pharmaexpert.ru/passonline/index.php) which is based on the identification of substructure features typical for active molecules. [28,29] Lipophilicity parameters clogP and clogD at pH 7.5 for synthesized compounds were calculated using Volsurf+ approach. [30] Classification models were built using decision tree algorithm See5, release 2.07.…”

Section: Antibacterial Activitymentioning

confidence: 99%

Synthesis and SAR Study of Novel Amidino 2-substituted Benzimidazoles as Potential Antibacterial Agents

Perin¹,

Starčević²,

Perić³

et al. 2017

Croat. Chem. Acta

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A series of novel 2-substituted benzimidazole derivatives were synthesized and their antibacterial activity was assessed against selected Gram-positive and Gram-negative bacteria. The specific moiety at the 2-position of the benzimidazole was extensively modified with several fused heterocyclic functional groups containing nitrogen and sulfur heteroatoms. In addition, the influence of different amidino groups at the position 5 of benzimidazole scaffold was evaluated. The values of clogP (a partition coefficient) and clogD7.5 (calculated distribution coefficient, pH 7.5) were determined and the lipophilic character of compounds has been found to be important parameter for the observed activity of the tested benzimidazole derivatives against Moraxella catarrhalis. The indolo 2-substituted benzimidazole 13a demonstrated solid activity against Staphylococcus aureus (MICs 16 µg/mL) and Moraxella catarralis (MICs 2 µg/mL) and represents promising lead molecule for further optimization.

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Probabilistic Approaches in Activity Prediction

Cited by 86 publications

References 99 publications

Application of molecular descriptors for recognition of phosphorylation sites in amino acid sequences

Application of molecular descriptors for recognition of phosphorylation sites in amino acid sequences

An efficient and convenient microwave-assisted chemical synthesis of (thio)xanthones with additional in vitro and in silico characterization

Synthesis and SAR Study of Novel Amidino 2-substituted Benzimidazoles as Potential Antibacterial Agents

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