Journal ArticleDOI
Chemography: the art of navigating in chemical space.
Tudor I. Oprea,Johan Gottfries +1 more
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ChemGPS scores are comparable across a large number of chemicals and do not change as new structures are predicted, making this tool a well-suited reference system for comparing multiple libraries and for keeping track of previously explored regions of the chemical space.Citations
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Discovery and resupply of pharmacologically active plant-derived natural products: A review.
Atanas G. Atanasov,Birgit Waltenberger,Eva-Maria Pferschy-Wenzig,Thomas Linder,Christoph Wawrosch,Pavel Uhrin,Veronika Temml,Limei Wang,Stefan Schwaiger,Elke H. Heiss,Judith M. Rollinger,Judith M. Rollinger,Daniela Schuster,Johannes M. Breuss,Valery N. Bochkov,Marko D. Mihovilovic,Brigitte Kopp,Rudolf Bauer,Verena M. Dirsch,Hermann Stuppner +19 more
TL;DR: While the intrinsic complexity of natural product-based drug discovery necessitates highly integrated interdisciplinary approaches, the reviewed scientific developments, recent technological advances, and research trends clearly indicate that natural products will be among the most important sources of new drugs in the future.
Journal ArticleDOI
Chemometrics in Metabonomics
TL;DR: An overview of how the underlying philosophy of chemometrics is integrated throughout metabonomic studies is provided, including the tools applied for linear modeling, for example, Statistical Experimental Design (SED), Principal Component Analysis (PCA), Partial least-squares (PLS), Orthogonal-PLS, and dynamic extensions thereof.
Journal ArticleDOI
Navigating chemical space for biology and medicine
TL;DR: What are the best strategies for identifying small molecules that modulate biological targets?
Journal ArticleDOI
Ultra-large library docking for discovering new chemotypes
Jiankun Lyu,Sheng Wang,Trent E. Balius,Isha Singh,Anat Levit,Yurii S. Moroz,Matthew J. O’Meara,Tao Che,Enkhjargal Algaa,Kateryna A. Tolmachova,Andrey A. Tolmachev,Brian K. Shoichet,Bryan L. Roth,John J. Irwin +13 more
TL;DR: Using a make-on-demand library that contains hundreds-of-millions of molecules, structure-based docking was used to identify compounds that, after synthesis and testing, are shown to interact with AmpC β-lactamase and the D4 dopamine receptor with high affinity.
Journal ArticleDOI
The chemical space project.
TL;DR: Beyond enumeration, understanding and exploiting GDBs (generated databases) led us to develop methods for virtual screening and visualization of very large databases in the form of a "periodic system of molecules" comprising six different fingerprint spaces, and the MQN- and SMIfp-Mapplet application for exploring color-coded principal component maps of GDB and other large databases.
References
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Journal ArticleDOI
Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges
Johann Gasteiger,Mario Marsili +1 more
TL;DR: In this article, a method for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems is presented, where only the connectivities of the atoms are considered.
Book
A User's Guide to Principal Components
TL;DR: In this paper, the authors present a directory of Symbols and Definitions for PCA, as well as some classic examples of PCA applications, such as: linear models, regression PCA of predictor variables, and analysis of variance PCA for Response Variables.
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How Long Is the Coast of Britain? Statistical Self-Similarity and Fractional Dimension
TL;DR: Geographical curves are so involved in their detail that their lengths are often infinite or, rather, undefinable; however, many are statistically "selfsimilar," meaning that each portion can be considered a reduced-scale image of the whole.
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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
TL;DR: The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values.
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Cross-Validatory Estimation of the Number of Components in Factor and Principal Components Models
TL;DR: In this article, the rank estimation of the rank A of the matrix Y, i.e., the estimation of how much of the data y ik is signal and how much is noise, is considered.