Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics
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2015
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A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL state-of-the-art molecular graphics. Students create a human serum albumin homology model with relatively high resolution at 1.77 angstrom (heavy atom model) and with reasonable values for bond lengths, angles, and dihedrals. The suggested tasks integrate different fundamental aspects of structural biology and protein modeling. Ramachandran plots and side chain rotamers are discussed. The assignments are shown to be good not only to teach homology modeling basics, but also to introduce several other concepts of structural bioinformatics such as protein sequence data mining, basic local alignment search tool (BLAST), and multiple sequence alignment. Homolo...gy modeling is demonstrated to be a cornerstone in molecular docking and drug design projects if the crystal structure of the protein of interest is not yet determined.
Ključne reči:
Upper-Division Undergraduate / Biochemistry / Chemoinformatics / Computer-Based Learning / Laboratory Instruction / Medicinal Chemistry / Molecular Modeling / Proteins/PeptidesIzvor:
Journal of Chemical Education, 2015, 92, 7, 1233-1237Izdavač:
- Amer Chemical Soc, Washington
Napomena:
- Supplementary material: http://cherry.chem.bg.ac.rs/handle/123456789/3385
DOI: 10.1021/ed500358f
ISSN: 0021-9584
WoS: 000358560700020
Scopus: 2-s2.0-84949186623
Kolekcije
Institucija/grupa
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Petrović, Dušan AU - Zlatović, Mario PY - 2015 UR - https://cherry.chem.bg.ac.rs/handle/123456789/1745 AB - A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL state-of-the-art molecular graphics. Students create a human serum albumin homology model with relatively high resolution at 1.77 angstrom (heavy atom model) and with reasonable values for bond lengths, angles, and dihedrals. The suggested tasks integrate different fundamental aspects of structural biology and protein modeling. Ramachandran plots and side chain rotamers are discussed. The assignments are shown to be good not only to teach homology modeling basics, but also to introduce several other concepts of structural bioinformatics such as protein sequence data mining, basic local alignment search tool (BLAST), and multiple sequence alignment. Homology modeling is demonstrated to be a cornerstone in molecular docking and drug design projects if the crystal structure of the protein of interest is not yet determined. PB - Amer Chemical Soc, Washington T2 - Journal of Chemical Education T1 - Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics VL - 92 IS - 7 SP - 1233 EP - 1237 DO - 10.1021/ed500358f ER -
@article{ author = "Petrović, Dušan and Zlatović, Mario", year = "2015", abstract = "A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL state-of-the-art molecular graphics. Students create a human serum albumin homology model with relatively high resolution at 1.77 angstrom (heavy atom model) and with reasonable values for bond lengths, angles, and dihedrals. The suggested tasks integrate different fundamental aspects of structural biology and protein modeling. Ramachandran plots and side chain rotamers are discussed. The assignments are shown to be good not only to teach homology modeling basics, but also to introduce several other concepts of structural bioinformatics such as protein sequence data mining, basic local alignment search tool (BLAST), and multiple sequence alignment. Homology modeling is demonstrated to be a cornerstone in molecular docking and drug design projects if the crystal structure of the protein of interest is not yet determined.", publisher = "Amer Chemical Soc, Washington", journal = "Journal of Chemical Education", title = "Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics", volume = "92", number = "7", pages = "1233-1237", doi = "10.1021/ed500358f" }
Petrović, D.,& Zlatović, M.. (2015). Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics. in Journal of Chemical Education Amer Chemical Soc, Washington., 92(7), 1233-1237. https://doi.org/10.1021/ed500358f
Petrović D, Zlatović M. Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics. in Journal of Chemical Education. 2015;92(7):1233-1237. doi:10.1021/ed500358f .
Petrović, Dušan , Zlatović, Mario, "Modeling Human Serum Albumin Tertiary Structure To Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics" in Journal of Chemical Education, 92, no. 7 (2015):1233-1237, https://doi.org/10.1021/ed500358f . .