Effect of ligand-binding on protein function
Julkaistu sarjassa
Jyväskylä studies in biological and environmental scienceTekijät
Päivämäärä
2014Oppiaine
Solu- ja molekyylibiologiaJulkaisija
University of JyväskyläISBN
978-951-39-5583-0ISSN Hae Julkaisufoorumista
1456-9701Julkaisuun sisältyy osajulkaisuja
- Article I: Postila P.A., Ylilauri M. & Pentikäinen O.T. 2011. Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations. Journal of Chemical Information and Modeling 51: 1037–1047. DOI: 10.1021/ci2000055
- Article II: Ylilauri M. & Pentikäinen O.T. 2012. Structural mechanism of N-methyl-D -aspartate receptor type 1 partial agonism. PLoS One 7 (10): e47604. DOI: 10.1371/journal.pone.0047604
- Article III: Ylilauri M. & Pentikäinen O.T. 2013. MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions. Journal of Chemical Information and Modeling 53: 2626-2633 . DOI: 10.1021/ci4002475
- Article IV: Ylilauri M., Mattila E., Nurminen E.M., Käpylä J., Niinivehmas S.P., Määttä J.A., Pentikäinen U., Ivaska J. & Pentikäinen O.T. 2013. Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone. Biochimica et Biophysica Acta 1834: 1988-1997. DOI: 10.1016/j.bbapap.2013.07.001
Asiasanat
tietokonesimulointi molekyylidynamiikka ionotrooppiset glutamaattireseptorit peptidiligandit iGluR FLNa TCPTP binding free energy filamin ionotropic glutamate receptor molecular dynamics T-cell protein tyrosine phosphatase proteiinit ligandit filamiinit sitoutuminen lääkesuunnittelu laskennallinen tiede simulointi laskennalliset menetelmät
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Samankaltainen aineisto
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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 ... -
Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers
Mironov, Vladimir; Shchugoreva, Irina A.; Artyushenko, Polina V.; Morozov, Dmitry; Borbone, Nicola; Oliviero, Giorgia; Zamay, Tatiana N.; Moryachkov, Roman V.; Kolovskaya, Olga S.; Lukyanenko, Kirill A.; Song, Yangling; Merkuleva, Iuliia A.; Zabluda, Vladimir N.; Peters, Georgy; Koroleva, Lyudmila S.; Veprintsev, Dmitry V.; Glazyrin, Yury E.; Volosnikova, Ekaterina A.; Belenkaya, Svetlana V.; Esina, Tatiana I.; Isaeva, Anastasiya A.; Nesmeyanova, Valentina S.; Shanshin, Daniil V.; Berlina, Anna N.; Komova, Nadezhda S.; Svetlichnyi, Valery A.; Silnikov, Vladimir N.; Shcherbakov, Dmitriy N.; Zamay, Galina S.; Zamay, Sergey S.; Smolyarova, Tatyana; Tikhonova, Elena P.; Chen, Kelvin H.-C.; Jeng, U-Ser; Condorelli, Gerolama; de Franciscis, Vittorio; Groenhof, Gerrit; Yang, Chaoyong; Moskovsky, Alexander A.; Fedorov, Dmitri G.; Tomilin, Felix N.; Tan, Weihong; Alexeev, Yuri; Berezovski, Maxim V.; Kichkailo, Anna S. (Wiley-VCH Verlag, 2022)Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable ... -
Computational studies of biomolecular screening and interactions
Niinivehmas, Sanna (University of Jyväskylä, 2015) -
Three proteins regulating integrin function - filamin, 14-3-3 and RIAM
Takala, Heikki (University of Jyväskylä, 2011) -
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 ...
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