ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors

Varnek, Alexandre; Fourches, Denis; Horvath, Dragos; Klimchuk, Olga; Gaudin, Cédric; Vayer, Philippe; Solov'ev, Vitaly P.; Hoonakker, Frank; Tetko, Igor V.; Marcou, Gilles

doi:10.2174/157340908785747465

Cited by 192 publications

(207 citation statements)

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“…[53] The data manager EdiSDF [35,46,54] was used to prepare data sets containing finally from 52 (Hg …”

Section: Data Setsmentioning

confidence: 99%

“…In order to overcome this problem, we have developed the COMET (COmplexation of METals) software [39] which implements previously elaborated QSPR models of stability constants (logK) of the 1:1 (M:L) complexes of diverse organic ligands with alkaline-earth (Sr 2+ , [33,35] , and UO 2 2+ [43] ) in water at 298 K and an ionic strength 0.1 M. All these models are based on substructural molecular fragments (SMF) [23,30,33] representing a subtype of the ISIDA descriptors. [46] SMF are subgraphs of molecular graph [30,47] whereas fragment occurrences are descriptor values. SMF descriptors are calculated solely from 2D chemical structures.…”

Section: Introductionmentioning

confidence: 99%

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New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln3+, Ag+, Zn2+, Cd2+ and Hg2+ with Organic Ligands in Water

Соловьев¹,

Tsivadze²,

Varnek³

2012

MHC

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In this paper, we propose a new definition of models applicability domain (AD) based on the selection of sufficient portion of individual QSPR models to be accepted for property prediction. Efficiency of this approach has been demonstrated in ensemble modeling of the stability constants logK of the 1:1 complexes of 17 lanthanide and transition metal ions (M) with various organic ligands (L) ) metal ions with sets of diverse organic molecules in aqueous solution at 298 K and an ionic strength 0.1 M. The models have been validated by external 5-fold crossvalidation procedure. The root mean squared error (RMSE) of predictions is similar to systematic errors in experimental data. This is twice smaller compared to earlier reported models for which "quorum control" AD has not been applied. Methods Data SetsThe experimental stability constant (logK) ) metal ions with diverse organic ligands in water were selected from the IUPAC Stability Constants Database (SC DB) (version 5.33, Academic Software) [15] at standard temperature 298 K and an ionic strength I = 0.1 M. Some logK values (around 15 %) were corrected to specified temperature and an ionic strength using the procedures included in SC DB.2D structures of ligands, names of metal ions and corresponding logK values resulted from searching in SC DB were converted into Structure -Data Files (SDF) served as an input in the MLR module of the ISIDA (In Silico Design and Data Analysis) /QSPR program.[53] The data manager EdiSDF [35,46,54] was used to prepare data sets containing finally from 52 (Hg

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“…[53] The data manager EdiSDF [35,46,54] was used to prepare data sets containing finally from 52 (Hg …”

Section: Data Setsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln3+, Ag+, Zn2+, Cd2+ and Hg2+ with Organic Ligands in Water

Соловьев¹,

Tsivadze²,

Varnek³

2012

MHC

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“…Fragment descriptors were calculated with ISIDA Fragmentor software [17,18] and they were filtered to discard those with zero or close to zero variance. Afterward, the mRMR algorithm [19] was employed to only keep the 250 more relevant descriptors.…”

Section: Resultsmentioning

confidence: 99%

“…The ISIDA Fragmentor software (freely available at http://infochim.ustrasbg.fr/spip.php?rubrique49) was used to calculate 2D fragment descriptors [17,18].…”

Section: Molecular Descriptorsmentioning

confidence: 99%

<strong>Virtual screening tailored ensembles of QSAR models for the discovery of dual A<sub>2A</sub> Adenosine Receptor Antagonists / Monoamine Oxidase B Inhibitors</strong>

Helguera

Pérez-Castillo

Cordeiro

et al. 2015

Proceedings of MOL2NET, International Conference on Multidisciplinary Sciences

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Virtual Screening methodologies have emerged as efficient alternatives for the discovery of new drug candidates. At the same time, ensemble methods are nowadays frequently used to overcome the limitations of employing a single model in ligand-based drug design. However, many applications of ensemble methods to this area do not consider important aspects related to both virtual screening and the modeling process. During the application of ensemble methods to virtual screening the proper validation of the models in virtual screening conditions is often neglected. Frequently no analysis is performed of the diversity of the ensemble members or no considerations regarding the applicability domain of the base model are made. In this research we propose a method employing genetic algorithms optimization for the generation of virtual SciForum Mol2Net, 2015, 1(Section B), pages 1-10, Proceedings 2 http://sciforum.net/conference/mol2net-1 screening tailored ensembles that address problems in the current applications of ensemble methods to virtual screening. The proposed methodology is successfully applied to the generation of ensemble models for the ligand-based virtual screening of dual target A2A adenosine receptor antagonists and MAO-B inhibitors as potential Parkinson's disease therapeutics. .

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“…The structures were encoded by ISIDA descriptors [12] representing atom centered fragments containing from 2 to 4 atoms in atom/bond sequences connected to the central atom.…”

Section: Methodsmentioning

confidence: 99%

Neighboring Structure Visualization on a Grid‐based Layout

Marcou

Horvath

Varnek

2017

Molecular Informatics

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Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi-or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts.

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ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors

Cited by 192 publications

References 0 publications

New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln3+, Ag+, Zn2+, Cd2+ and Hg2+ with Organic Ligands in Water

New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln3+, Ag+, Zn2+, Cd2+ and Hg2+ with Organic Ligands in Water

<strong>Virtual screening tailored ensembles of QSAR models for the discovery of dual A<sub>2A</sub> Adenosine Receptor Antagonists / Monoamine Oxidase B Inhibitors</strong>

Neighboring Structure Visualization on a Grid‐based Layout

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