Editing Protein structure prediction (section)

===Other improvements===
It is reported that in addition to the protein sequence, secondary structure formation depends on other factors. For example, it is reported that secondary structure tendencies depend also on local environment,<ref name="a0">{{cite journal |vauthors=Zhong L, Johnson WC |title=Environment affects amino acid preference for secondary structure |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=89 |issue=10 |pages=4462–5 |date=May 1992 |pmid=1584778 |pmc=49102 |doi=10.1073/pnas.89.10.4462 |bibcode=1992PNAS...89.4462Z |doi-access=free}}</ref> solvent accessibility of residues,<ref name="a1">{{cite journal |vauthors=Macdonald JR, Johnson WC |title=Environmental features are important in determining protein secondary structure |journal=Protein Science |volume=10 |issue=6 |pages=1172–7 |date=June 2001 |pmid=11369855 |pmc=2374018 |doi=10.1110/ps.420101}}</ref> protein structural class,<ref name="a2">{{cite journal |vauthors=Costantini S, Colonna G, Facchiano AM |title=Amino acid propensities for secondary structures are influenced by the protein structural class |journal=Biochemical and Biophysical Research Communications |volume=342 |issue=2 |pages=441–51 |date=April 2006 |pmid=16487481 |doi=10.1016/j.bbrc.2006.01.159}}</ref> and even the organism from which the proteins are obtained.<ref name="a3">{{cite journal |vauthors=Marashi SA, Behrouzi R, Pezeshk H |title=Adaptation of proteins to different environments: a comparison of proteome structural properties in Bacillus subtilis and Escherichia coli |journal=Journal of Theoretical Biology |volume=244 |issue=1 |pages=127–32 |date=January 2007 |pmid=16945389 |doi=10.1016/j.jtbi.2006.07.021 |bibcode=2007JThBi.244..127M}}</ref> Based on such observations, some studies have shown that secondary structure prediction can be improved by addition of information about protein structural class,<ref name="m">{{cite journal |vauthors=Costantini S, Colonna G, Facchiano AM |title=PreSSAPro: a software for the prediction of secondary structure by amino acid properties |journal=Computational Biology and Chemistry |volume=31 |issue=5–6 |pages=389–92 |date=October 2007 |pmid=17888742 |doi=10.1016/j.compbiolchem.2007.08.010}}</ref> residue accessible surface area<ref name="P">{{cite journal |vauthors=Momen-Roknabadi A, Sadeghi M, Pezeshk H, Marashi SA |title=Impact of residue accessible surface area on the prediction of protein secondary structures |journal=BMC Bioinformatics |volume=9 |pages=357 |date=August 2008 |pmid=18759992 |pmc=2553345 |doi=10.1186/1471-2105-9-357 |doi-access=free}}</ref><ref name="Ph">{{cite journal |vauthors=Adamczak R, Porollo A, Meller J |title=Combining prediction of secondary structure and solvent accessibility in proteins |journal=Proteins |volume=59 |issue=3 |pages=467–75 |date=May 2005 |pmid=15768403 |doi=10.1002/prot.20441 |s2cid=13267624}}</ref> and also [[contact number]] information.<ref name="az">{{cite journal |vauthors=Lakizadeh A, Marashi SA |year=2009 |url=http://www.excli.de/vol8/lakizadeh_03_2009/lakizadeh_250309a_proof.pdf |title=Addition of contact number information can improve protein secondary structure prediction by neural networks |journal=Excli J. |volume=8 |pages=66–73}}</ref>