Reference#
Mark Howarth. Say it with proteins: an alphabet of crystal structures. Nature Structural & Molecular Biology, 22(5):349–349, 2015. doi:10.1038/nsmb.3011.
Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng, Gregory S. Couch, Tristan I. Croll, John H. Morris, and Thomas E. Ferrin. Ucsf chimerax: structure visualization for researchers, educators, and developers. Protein Science, 30(1):70–82, 2021. doi:10.1002/pro.3943.
David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, and Alexander S Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1):W431–W437, 2021. doi:10.1093/nar/gkab314.
Helen M. Berman, Stephen K. Burley, Wah Chiu, Andrej Sali, Alexei Adzhubei, Philip E. Bourne, Stephen H. Bryant, Roland L. Dunbrack, Krzysztof Fidelis, Joachim Frank, Adam Godzik, Kim Henrick, Andrzej Joachimiak, Bernard Heymann, David Jones, John L. Markley, John Moult, Gaetano T. Montelione, Christine Orengo, Michael G. Rossmann, Burkhard Rost, Helen Saibil, Torsten Schwede, Daron M. Standley, and John D. Westbrook. Outcome of a workshop on archiving structural models of biological macromolecules. Structure, 14(8):1211–1217, 2006. doi:10.1016/j.str.2006.06.005.
Dmitrij Frishman and Patrick Argos. Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Bioinformatics, 23(4):566–579, 1995. doi:https://doi.org/10.1002/prot.340230412.
Wolfgang Kabsch and Christian Sander. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12):2577–2637, 1983. doi:https://doi.org/10.1002/bip.360221211.
Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E. Felberg, David H. Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li, David W. Gohara, Todd Dolinsky, Robert Konecny, David R. Koes, Jens Erik Nielsen, Teresa Head-Gordon, Weihua Geng, Robert Krasny, Guo-Wei Wei, Michael J. Holst, J. Andrew McCammon, and Nathan A. Baker. Improvements to the apbs biomolecular solvation software suite. Protein Science, 27(1):112–128, 2018. doi:https://doi.org/10.1002/pro.3280.
Christopher J. Williams, Jeffrey J. Headd, Nigel W. Moriarty, Michael G. Prisant, Lizbeth L. Videau, Lindsay N. Deis, Vishal Verma, Daniel A. Keedy, Bradley J. Hintze, Vincent B. Chen, Swati Jain, Steven M. Lewis, W. Bryan Arendall III, Jack Snoeyink, Paul D. Adams, Simon C. Lovell, Jane S. Richardson, and David C. Richardson. Molprobity: more and better reference data for improved all-atom structure validation. Protein Science, 27(1):293–315, 2018. doi:https://doi.org/10.1002/pro.3330.
E. Krissinel and K. Henrick. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D, 60(12 Part 1):2256–2268, 2004. doi:https://doi.org/10.1107/S0907444904026460.