content

topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.bib

@@ -13,7 +13,7 @@ @article{zierep_sempi_2020
 	year = {2020},
 	pmid = {33383692},
 	pmcid = {PMC7823522},
-	keywords = {machine learning, natural compounds, nonribosomal peptides, polyketides, secondary metabolites},
+	keywords = {machine learning, polyketides, secondary metabolites, natural compounds, nonribosomal peptides},
 	pages = {13},
 	file = {Full Text:/home/paul/Zotero/storage/ZHE7YEGD/Zierep et al. - 2020 - SeMPI 2.0-A Web Server for PKS and NRPS Prediction.pdf:application/pdf},
 }
@@ -65,6 +65,43 @@ @article{adamek_mining_2017
 	author = {Adamek, Martina and Spohn, Marius and Stegmann, Evi and Ziemert, Nadine},
 	year = {2017},
 	pmid = {27873244},
-	keywords = {Antibiotics, antiSMASH, Base Sequence, Biosynthesis, Cluster boundaries, Data Mining, Gene cluster families, Genome mining, Genome, Bacterial, INBEKT, Multigene Family, Prioritization, Secondary Metabolism, Secondary metabolite gene cluster},
+	keywords = {Biosynthesis, Antibiotics, Data Mining, Multigene Family, Secondary Metabolism, Base Sequence, Genome, Bacterial, Genome mining, antiSMASH, Cluster boundaries, Gene cluster families, INBEKT, Prioritization, Secondary metabolite gene cluster},
 	pages = {23--47},
 }
+
+@article{muegge_overview_2016,
+	title = {An overview of molecular fingerprint similarity search in virtual screening},
+	volume = {11},
+	issn = {1746-045X},
+	doi = {10.1517/17460441.2016.1117070},
+	abstract = {INTRODUCTION: A central premise of medicinal chemistry is that structurally similar molecules exhibit similar biological activities. Molecular fingerprints encode properties of small molecules and assess their similarities computationally through bit string comparisons. Based on the similarity to a biologically active template, molecular fingerprint methods allow for identifying additional compounds with a higher chance of displaying similar biological activities against the same target - a process commonly referred to as virtual screening (VS).
+AREAS COVERED: This article focuses on fingerprint similarity searches in the context of compound selection for enhancing hit sets, comparing compound decks, and VS. In addition, the authors discuss the application of fingerprints in predictive modeling.
+EXPERT OPINION: Fingerprint similarity search methods are especially useful in VS if only a few unrelated ligands are known for a given target and therefore more complex and information rich methods such as pharmacophore searches or structure-based design are not applicable. In addition, fingerprint methods are used in characterizing properties of compound collections such as chemical diversity, density in chemical space, and content of biologically active molecules (biodiversity). Such assessments are important for deciding what compounds to experimentally screen, to purchase, or to assemble in a virtual compound deck for in silico screening or de novo design.},
+	language = {eng},
+	number = {2},
+	journal = {Expert Opinion on Drug Discovery},
+	author = {Muegge, Ingo and Mukherjee, Prasenjit},
+	year = {2016},
+	pmid = {26558489},
+	keywords = {Chemistry, Pharmaceutical, Compound acquisition, Computer Simulation, Computer-Aided Design, Drug Design, hit expansion, Humans, Models, Molecular, Molecular Targeted Therapy, Pharmaceutical Preparations, pharmacophore fingerprint, predictive modeling, scaffold hopping, Structure-Activity Relationship},
+	pages = {137--148},
+}
+
+@article{capecchi_one_2020,
+	title = {One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome},
+	volume = {12},
+	issn = {1758-2946},
+	shorttitle = {One molecular fingerprint to rule them all},
+	url = {https://doi.org/10.1186/s13321-020-00445-4},
+	doi = {10.1186/s13321-020-00445-4},
+	abstract = {Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecules such as drugs, while atom-pair fingerprints are preferable for large molecules such as peptides. However, no available fingerprint achieves good performance on both classes of molecules.},
+	number = {1},
+	urldate = {2024-02-20},
+	journal = {Journal of Cheminformatics},
+	author = {Capecchi, Alice and Probst, Daniel and Reymond, Jean-Louis},
+	month = jun,
+	year = {2020},
+	keywords = {Chemical space, Databases, Locality sensitive hashing, Molecular fingerprints, Virtual screening},
+	pages = {43},
+	file = {Full Text PDF:/home/paul/Zotero/storage/68LLX7XQ/Capecchi et al. - 2020 - One molecular fingerprint to rule them all drugs,.pdf:application/pdf;Snapshot:/home/paul/Zotero/storage/C5F3WE2U/s13321-020-00445-4.html:text/html},
+}