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InterMetalDB.lyx
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
\save_transient_properties true
\origin unavailable
\textclass classicthesis
\begin_preamble
\usepackage{pdfpages}
\end_preamble
\use_default_options true
\maintain_unincluded_children false
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\end_header
\begin_body
\begin_layout Chapter
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites
in Macromolecules with Structural Information
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
chaptermark{
\backslash
protect
\backslash
parbox{0.9
\backslash
linewidth}{InterMetalDB -- A Database of Intermolecular Metal Binding Sites}}
\end_layout
\end_inset
\end_layout
\begin_layout Standard
\begin_inset CommandInset label
LatexCommand label
name "chap:InterMetalDB"
\end_inset
\end_layout
\begin_layout Standard
\shape smallcaps
Józef Ba Tran and Artur Krężel
\shape default
\begin_inset Newline newline
\end_inset
\begin_inset Flex CT - Spaced Low Small Caps
status open
\begin_layout Plain Layout
Department of Chemical Biology, Faculty of Biotechnology, University of
Wrocław, F.
Joliot-Curie 14a, 50-383 Wrocław, Poland
\end_layout
\end_inset
\begin_inset Newline newline
\end_inset
\shape italic
Journal of Proteome Research
\shape default
\size small
\size default
2021 20(4), 1889–1901.
\end_layout
\begin_layout Standard
\begin_inset VSpace medskip
\end_inset
\end_layout
\begin_layout Section
Brief history and bibliometric data
\end_layout
\begin_layout Standard
The work on the
\begin_inset CommandInset citation
LatexCommand citetitle
key "Kocyla2021"
literal "true"
\end_inset
(
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Galvanization-of-Protein-Protein"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
), among other things, included the preparation of the data set containing
all deposited
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{zppi}
\end_layout
\end_inset
in the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{rcsb}
\end_layout
\end_inset
.
To manipulate
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{pdb}
\end_layout
\end_inset
files, and filter for
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{zppi}
\end_layout
\end_inset
I have used the
\family typewriter
BioPython
\family default
library
\begin_inset CommandInset citation
LatexCommand citep
key "Cock2009"
literal "true"
\end_inset
.
My primary school art teacher used to say
\begin_inset Quotes eld
\end_inset
If something is for everything, it's really for nothing.
\begin_inset Quotes erd
\end_inset
, the similar is with
\family typewriter
BioPython
\family default
, which has a wide range of tools used in bioinformatics, however, the offered
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{api}
\end_layout
\end_inset
is rather clumsy in use, and
\family typewriter
BioPython
\family default
itself lacks some more advanced functions to handle
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{pdb}
\end_layout
\end_inset
files.
Combined with the restructuration of the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{rcsb}
\end_layout
\end_inset
search
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{api}
\end_layout
\end_inset
and often questions from Ania Kocyła if the data set is ready I knew that
the next project that will involve data from
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{rcsb}
\end_layout
\end_inset
will have to offer an easier in use libraries.
Around this time a new
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{python}
\end_layout
\end_inset
library emerged that allowed for efficient and easy
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{pdb}
\end_layout
\end_inset
file parsing—
\family typewriter
atomium
\family default
\begin_inset CommandInset citation
LatexCommand citep
key "Ireland2020"
literal "true"
\end_inset
, which allowed for easy manipulation with
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{pdb}
\end_layout
\end_inset
files, building a better logic behind the database, and making the whole
process scalable.
\begin_inset Note Note
status open
\begin_layout Plain Layout
tu może coś więcej napisać?
\end_layout
\end_inset
\end_layout
\begin_layout Standard
The article describing InterMetalDB was accepted and published only after
minor revision in the
\shape italic
Journal of Proteome Research
\emph on
(
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{if}
\end_layout
\end_inset
of
\shape default
\emph default
5.370
\shape italic
\emph on
, March 6, 2023) in 2021, and to date (
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
today
\end_layout
\end_inset
) the article was cited
\shape default
\emph default
\begin_inset ERT
status collapsed
\begin_layout Plain Layout
\backslash
begin{pycode}[sessionA]
\end_layout
\begin_layout Plain Layout
from scholarly import scholarly
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num2words = {1: 'one',
\end_layout
\begin_layout Plain Layout
2: 'two',
\end_layout
\begin_layout Plain Layout
3: 'three',
\end_layout
\begin_layout Plain Layout
4: 'four',
\end_layout
\begin_layout Plain Layout
5: 'five',
\end_layout
\begin_layout Plain Layout
6: 'six',
\end_layout
\begin_layout Plain Layout
7: 'seven',
\end_layout
\begin_layout Plain Layout
8: 'eight',
\end_layout
\begin_layout Plain Layout
9: 'nine',
\end_layout
\begin_layout Plain Layout
10: 'ten',
\end_layout
\begin_layout Plain Layout
11: 'eleven',
\end_layout
\begin_layout Plain Layout
12: 'twelve',
\end_layout
\begin_layout Plain Layout
13: 'thirteen',
\end_layout
\begin_layout Plain Layout
14: 'fourteen',
\end_layout
\begin_layout Plain Layout
15: 'fifteen',
\end_layout
\begin_layout Plain Layout
16: 'sixteen',
\end_layout
\begin_layout Plain Layout
17: 'seventeen',
\end_layout
\begin_layout Plain Layout
18: 'eighteen',
\end_layout
\begin_layout Plain Layout
19: 'nineteen',
\end_layout
\begin_layout Plain Layout
20: 'twenty',
\end_layout
\begin_layout Plain Layout
30: 'thirty',
\end_layout
\begin_layout Plain Layout
40: 'forty',
\end_layout
\begin_layout Plain Layout
50: 'fifty',
\end_layout
\begin_layout Plain Layout
60: 'sixty',
\end_layout
\begin_layout Plain Layout
70: 'seventy',
\end_layout
\begin_layout Plain Layout
80: 'eighty',
\end_layout
\begin_layout Plain Layout
90: 'ninety',
\end_layout
\begin_layout Plain Layout
0: 'zero'}
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
def n2w(n):
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return (num2words[n])
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
try:
\end_layout
\begin_layout Plain Layout
return ((num2words[n-n % 10]) + ' ' + (num2words[n % 10].lower()))
\end_layout
\begin_layout Plain Layout
except KeyError:
\end_layout
\begin_layout Plain Layout
return ('Number out of range')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
search_query = scholarly.search_single_pub(
\end_layout
\begin_layout Plain Layout
'InterMetalDB: A Database and Browser of Intermolecular Metal Binding
Sites in Macromolecules with Structural Information')
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
num_citations = search_query['num_citations']
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
if num_citations <= 10:
\end_layout
\begin_layout Plain Layout
print(f' {n2w(num_citations)} times.')
\end_layout
\begin_layout Plain Layout
else:
\end_layout
\begin_layout Plain Layout
print(f' {num_citations} times.')
\end_layout
\begin_layout Plain Layout
\backslash
end{pycode}
\end_layout
\begin_layout Plain Layout
\end_layout
\end_inset
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status open
\begin_layout Plain Layout
https://scholar.google.com/
\end_layout
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Section
Summary
\end_layout
\begin_layout Standard
The fact that the metal ions can be bound at the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{interface}
\end_layout
\end_inset
that is created by two or more interacting macromolecules has been missing
interest from researchers (see
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Galvanization-of-Protein-Protein"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
).
The first systematic review of metal ions bound at protein-protein
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{interface}
\end_layout
\end_inset
was published in 2014
\begin_inset CommandInset citation
LatexCommand citep
key "Song2014"
literal "true"
\end_inset
, next, similar article (which was in part my creation) was published seven
years later, however, the article was concerning only intermolecularly
bound Zn(II) ions.
\begin_inset CommandInset citation
LatexCommand citep
key "Kocyla2021"
literal "true"
\end_inset
This stands in opposition to studies devoted to complexes with stoichiometry
of 1:1 – similar database surveys, generally concerning Zn(II)
\begin_inset Foot
status collapsed
\begin_layout Plain Layout
Probably due to its unique properties and abundance in
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
gls{proteome}
\end_layout
\end_inset
.
See
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Zinc proteome"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
.
\end_layout
\end_inset
, were done numerously in the past.
\begin_inset CommandInset citation
LatexCommand citep
key "Alberts1998,Auld2001,Patel2007,Dokmanic2008,Zheng2008,Lee2008,Hsin2008,Sousa2009,Andreini2011,Laitaoja2013"
literal "true"
\end_inset
As mentioned in
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Galvanization-of-Protein-Protein"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
one of the biggest pitfalls of such studies is the fact that simultaneously
with the publication of an article, the meticulously gathered, and classified
\begin_inset Marginal
status open
\begin_layout Plain Layout
\begin_inset CommandInset citation
LatexCommand citeauthor
key "Laitaoja2013"
literal "true"
\end_inset
have manually analyzed around 7800 Zn(II)-binding sites!
\begin_inset CommandInset citation
LatexCommand citep
key "Laitaoja2013"
literal "true"
\end_inset
\end_layout
\end_inset
knowledge is no longer updated, combined together with the fact that usually
the generated data set and the methodology is not easily and publicly available
makes such studies fleetly outdated.
This observation, which happened to occur to me during my work on the
\begin_inset CommandInset citation
LatexCommand citetitle
key "Kocyla2021"
literal "true"
\end_inset
(
\begin_inset Flex CT - auto cross-reference
status open
\begin_layout Plain Layout
\begin_inset CommandInset ref
LatexCommand labelonly
reference "chap:Galvanization-of-Protein-Protein"
plural "false"
caps "false"
noprefix "false"
\end_inset
\end_layout
\end_inset
), sprouted into an idea that the data set I will generate should be easily
available to anyone, free of charge and updated even after the publication
of the article.
This idea growth further, eventually bore fruit –
\begin_inset CommandInset citation
LatexCommand citetitle
key "Tran2021"
literal "true"
\end_inset
\begin_inset Foot
status open
\begin_layout Plain Layout
\begin_inset Flex URL
status open
\begin_layout Plain Layout
https://intermetaldb.biotech.uni.wroc.pl/
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\end_inset
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.
\end_layout
\begin_layout Standard
My intention for the creation of InterMetalDB was to provide a tool, which
would make researchers aware that macromolecules can bind metal ions at
the
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
glspl{interface}
\end_layout
\end_inset