Computational studies of biomolecular screening and interactions
Julkaistu sarjassa
Jyväskylä studies in biological and environmental scienceTekijät
Päivämäärä
2015Oppiaine
Solu- ja molekyylibiologiaJulkaisija
University of JyväskyläISBN
978-951-39-6382-8ISSN Hae Julkaisufoorumista
1456-9701Julkaisuun sisältyy osajulkaisuja
- Article I: Niinivehmas S.P.*, Virtanen S.I.*, Lehtonen J.V., Postila P.A. & Pentikäinen O.T. 2011. Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors. Journal of Chemical Information and Modeling 51: 1353-1363. DOI: 10.1021/ci1004527
- Article II: Niinivehmas S.P.*, Manivannan E.*, Rauhamäki S., Huuskonen J. & Pentikäinen O.T. 2016. Identification of estrogen receptor α ligands with virtual screening techniques. Journal of Molecular Graphics and Modelling 64, March, 30–39 DOI: 10.1016/j.jmgm.2015.12.006
- Article III: Niinivehmas S.P., Salokas K., Lätti S., Raunio H. & Pentikäinen O.T. 2015. Ultrafast protein structure-based virtual screening with Panther. Journal of Computer-Aided Molecular Design 10: 989-1006. DOI: 10.1007/s10822-015-9870-3
- Article IV: Virtanen S.*, Niinivehmas S.P.* & Pentikäinen O.T. 2015. Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening. Journal of Molecular Graphics and Modelling 62 (November) 203-318. DOI:10.1016/j.jmgm.2015.10.012 .
- Article V: Niinivehmas S.P. & Pentikäinen O.T. 2015. Reliability of virtual screening methods in prediction of PDE4B-inhibitor activity. Current Drug Discovery Technologies 12: 117-26. DOI: 10.2174/1570163812666150702123018
- Article VI: Sergelius C., Niinivehmas S., Maula T., Kurita M., Yamaguchi S., Yamamoto T., Katsumura S., Pentikäinen O.T. & Slotte J.P. 2012. Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus. Biochimica et Biophysica Acta 1818: 474-480. DOI: 10.1016/j.bbamem.2011.10.013
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Virtual screening : development of a novel structure-based method
Virtanen, Salla (University of Jyväskylä, 2013) -
A Practical Perspective : The Effect of Ligand Conformers on the Negative Image-Based Screening
Ahinko, Mira; Kurkinen, Sami; Niinivehmas, Sanna; Pentikäinen, Olli; Postila, Pekka (MDPI Center, 2019)Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein’s ... -
Structure and IR Spectroscopic Properties of HNCO Complexes with SO2 Isolated in Solid Argon
Krupa, Justyna; Wierzejewska, Maria; Lundell, Jan (MDPI AG, 2021)FTIR spectroscopy was combined with the matrix isolation technique and quantum chemical calculations with the aim of studying complexes of isocyanic acid with sulfur dioxide. The structures of the HNCO⋯SO2 complexes of ... -
Effect of ligand-binding on protein function
Ylilauri, Mikko (University of Jyväskylä, 2014) -
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
Ahinko, Mira; Niinivehmas, Sanna; Jokinen, Elmeri; Pentikäinen, Olli (Wiley-Blackwell Publishing, Inc., 2019)The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be ...
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