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Methods in molecular biology (Clifton, N.J.), 2011, Volume 672, pp. 261 - 298
This chapter is a review of the most recent developments in the field of pharmacophore modeling, covering both methodology and application. Pharmacophore-based... 
Receptors, Drug - chemistry | User-Computer Interface | Chemistry, Pharmaceutical - methods | Computer Simulation | Humans | Molecular Conformation | Drug Design | Models, Molecular | Protein Binding | Ligands | Proteins - chemistry
Journal Article
Journal of computer-aided molecular design, ISSN 0920-654X, 08/2019, pp. 1 - 11
Generative topographic mapping was used to investigate the possibility to diversify the in-house compounds collection of Boehringer Ingelheim (BI). For this... 
Substructures | Organic chemistry | Topography | Data bases | Biological activity | Topographic mapping
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2013, Volume 53, Issue 1, p. 88
  S4MPLE is a conformational sampling tool, based on a hybrid genetic algorithm, simulating one (conformer enumeration) or more molecules (docking). Energy... 
Proteins | Research & development--R&D | Ligands | Molecular biology | Crystallography | Sampling techniques
Journal Article
MOLECULES, ISSN 1420-3049, 06/2019, Volume 24, Issue 12, p. 2269
Following previous efforts to render the Conformational Space (CS) of flexible compounds by Generative Topographic Mapping (GTM), this polyvalent mapping... 
docking | PROTEIN-LIGAND ENTITIES | contact fingerprints | BIOCHEMISTRY & MOLECULAR BIOLOGY | generative topographic mapping | FRAGMENT | S4MPLE-SAMPLER | conformational space maps | CHEMISTRY, MULTIDISCIPLINARY
Journal Article
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 09/2018, Volume 32, Issue 9, pp. 877 - 888
Ligand affinity prediction from docking simulations is usually performed by means of highly empirical and diverse protocols. These protocols often involve the... 
Docking | Scoring | Force field calculations | Gold | Computer simulation | Calibration | Hydrophobicity | Complexity | Proteins | Solvation | Machine learning | Affinity | Ligands | Mathematical models | Binding sites
Journal Article
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 11/2017, Volume 31, Issue 11, pp. 961 - 977
The analysis of structure–activity relationships (SARs) becomes rather challenging when large and heterogeneous compound data sets are studied. In such cases,... 
Chemistry | Physical Chemistry | Generative topographic mapping | Chemical space networks | Animal Anatomy / Morphology / Histology | Matched molecular pair | Structure–activity relationships | Computer Applications in Chemistry | Datasets | Visualization | Landscape | Molecular structure | Data sets | Machine learning | Topographic mapping
Journal Article
Environmental Health Perspectives, ISSN 0091-6765, 07/2016, Volume 124, Issue 7, pp. 1023 - 1033
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2016, Volume 56, Issue 1, p. 6
  In this paper, we demonstrate that the kernel target alignment (KTA) parameter can efficiently be used to estimate the relevance of molecular descriptors for... 
Measurement | Molecules | Regression analysis | Comparative analysis
Journal Article
JOURNAL OF CHEMICAL INFORMATION AND MODELING, ISSN 1549-9596, 04/2019, Volume 59, Issue 4, pp. 1472 - 1485
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2019, Volume 59, Issue 1, pp. 564 - 572
Universal generative topographic maps (GTMs) provide two-dimensional representations of chemical space selected for their "polypharmacological competence",... 
SPACE | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | ISIDA | FRAGMENT | COMPUTER SCIENCE, INFORMATION SYSTEMS | CHEMISTRY, MULTIDISCIPLINARY | Decoys | Organic chemistry | Screening | Topographic maps | Maps | Landscape | Trustworthiness | Topography | Predictions | Ligands
Journal Article
Journal Article
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 03/2019, Volume 33, Issue 3, pp. 331 - 343
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 07/2009, Volume 49, Issue 7, pp. 1762 - 1776
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 03/2019, Volume 59, Issue 3, pp. 1182 - 1196
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 08/2016, Volume 56, Issue 8, p. 1438
  Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set,... 
Topography | Mapping | Antiviral drugs | Data bases
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2019, Volume 59, Issue 4, pp. 1472 - 1485
We recently reported an integrated fragment-based optimization strategy called DOTS (Diversity Oriented Target-focused Synthesis) that combines automated... 
Life Sciences | Quantitative Methods
Journal Article