%% BioMed_Central_Bib_Style_v1.01

\begin{thebibliography}{21}
% BibTex style file: bmc-mathphys.bst (version 2.1), 2014-07-24
\ifx \bisbn   \undefined \def \bisbn  #1{ISBN #1}\fi
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\ifx \bvolume  \undefined \def \bvolume#1{\textbf{#1}}\fi
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\ifx \burl  \undefined \def \burl#1{\textsf{#1}}\fi
\ifx \doiurl  \undefined \def \doiurl#1{\textsf{#1}}\fi
\ifx \betal  \undefined \def \betal{\textit{et al.}}\fi
\ifx \binstitute  \undefined \def \binstitute#1{#1}\fi
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\ifx \url \undefined \def \url#1{\textsf{#1}}\fi
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\ifx \arxivurl  \undefined \def \arxivurl#1{\textsf{#1}}\fi
\csname PreBibitemsHook\endcsname

%%% 1
\bibitem{marks2012protein}
\begin{barticle}
\bauthor{\bsnm{Marks}, \binits{D.S.}},
\bauthor{\bsnm{Hopf}, \binits{T.A.}},
\bauthor{\bsnm{Sander}, \binits{C.}}:
\batitle{Protein structure prediction from sequence variation}.
\bjtitle{Nature biotechnology}
\bvolume{30}(\bissue{11}),
\bfpage{1072}
(\byear{2012})
\end{barticle}
\endbibitem

%%% 2
\bibitem{paes2012gh11}
\begin{barticle}
\bauthor{\bsnm{Pa{\"e}s}, \binits{G.}},
\bauthor{\bsnm{Berrin}, \binits{J.-G.}},
\bauthor{\bsnm{Beaugrand}, \binits{J.}}:
\batitle{Gh11 xylanases: structure/function/properties relationships and
  applications}.
\bjtitle{Biotechnology advances}
\bvolume{30}(\bissue{3}),
\bfpage{564}--\blpage{592}
(\byear{2012})
\end{barticle}
\endbibitem

%%% 3
\bibitem{wu2018enhancement}
\begin{barticle}
\bauthor{\bsnm{Wu}, \binits{X.}},
\bauthor{\bsnm{Tian}, \binits{Z.}},
\bauthor{\bsnm{Jiang}, \binits{X.}},
\bauthor{\bsnm{Zhang}, \binits{Q.}},
\bauthor{\bsnm{Wang}, \binits{L.}}:
\batitle{Enhancement in catalytic activity of aspergillus niger xynb by
  selective site-directed mutagenesis of active site amino acids}.
\bjtitle{Applied microbiology and biotechnology}
\bvolume{102}(\bissue{1}),
\bfpage{249}--\blpage{260}
(\byear{2018})
\end{barticle}
\endbibitem

%%% 4
\bibitem{lin2011prediction}
\begin{barticle}
\bauthor{\bsnm{Lin}, \binits{H.}},
\bauthor{\bsnm{Chen}, \binits{W.}}:
\batitle{Prediction of thermophilic proteins using feature selection
  technique}.
\bjtitle{Journal of microbiological methods}
\bvolume{84}(\bissue{1}),
\bfpage{67}--\blpage{70}
(\byear{2011})
\end{barticle}
\endbibitem

%%% 5
\bibitem{van2015hydrophobic}
\begin{barticle}
\bauthor{\bparticle{van} \bsnm{Dijk}, \binits{E.}},
\bauthor{\bsnm{Hoogeveen}, \binits{A.}},
\bauthor{\bsnm{Abeln}, \binits{S.}}:
\batitle{The hydrophobic temperature dependence of amino acids directly
  calculated from protein structures}.
\bjtitle{PLoS computational biology}
\bvolume{11}(\bissue{5}),
\bfpage{1004277}
(\byear{2015})
\end{barticle}
\endbibitem

%%% 6
\bibitem{pucci2014stability}
\begin{barticle}
\bauthor{\bsnm{Pucci}, \binits{F.}},
\bauthor{\bsnm{Rooman}, \binits{M.}}:
\batitle{Stability curve prediction of homologous proteins using
  temperature-dependent statistical potentials}.
\bjtitle{PLoS computational biology}
\bvolume{10}(\bissue{7}),
\bfpage{1003689}
(\byear{2014})
\end{barticle}
\endbibitem

%%% 7
\bibitem{pucci2017scoop}
\begin{barticle}
\bauthor{\bsnm{Pucci}, \binits{F.}},
\bauthor{\bsnm{Kwasigroch}, \binits{J.M.}},
\bauthor{\bsnm{Rooman}, \binits{M.}}:
\batitle{Scoop: an accurate and fast predictor of protein stability curves as a
  function of temperature}.
\bjtitle{Bioinformatics}
\bvolume{33}(\bissue{21}),
\bfpage{3415}--\blpage{3422}
(\byear{2017})
\end{barticle}
\endbibitem

%%% 8
\bibitem{kc2016recent}
\begin{barticle}
\bauthor{\bsnm{Kc}, \binits{D.B.}}:
\batitle{Recent advances in sequence-based protein structure prediction}.
\bjtitle{Briefings in bioinformatics}
\bvolume{18}(\bissue{6}),
\bfpage{1021}--\blpage{1032}
(\byear{2016})
\end{barticle}
\endbibitem

%%% 9
\bibitem{liu2012importance}
\begin{botherref}
\oauthor{\bsnm{Liu}, \binits{S.}}:
Importance of improving scoring methods in predicting protein free-energy
  changes,
600--603
(2012)
\end{botherref}
\endbibitem

%%% 10
\bibitem{malinka2015prediction}
\begin{bchapter}
\bauthor{\bsnm{Malinka}, \binits{F.}}:
\bctitle{Prediction of protein stability changes upon one-point mutations using
  machine learning}.
In: \bbtitle{Proceedings of the 2015 Conference on Research in Adaptive and
  Convergent Systems},
pp. \bfpage{102}--\blpage{107}
(\byear{2015}).
\bcomment{ACM}
\end{bchapter}
\endbibitem

%%% 11
\bibitem{dehouck2011popmusic}
\begin{barticle}
\bauthor{\bsnm{Dehouck}, \binits{Y.}},
\bauthor{\bsnm{Kwasigroch}, \binits{J.M.}},
\bauthor{\bsnm{Gilis}, \binits{D.}},
\bauthor{\bsnm{Rooman}, \binits{M.}}:
\batitle{Popmusic 2.1: a web server for the estimation of protein stability
  changes upon mutation and sequence optimality}.
\bjtitle{BMC bioinformatics}
\bvolume{12}(\bissue{1}),
\bfpage{151}
(\byear{2011})
\end{barticle}
\endbibitem

%%% 12
\bibitem{wijma2014computationally}
\begin{barticle}
\bauthor{\bsnm{Wijma}, \binits{H.J.}},
\bauthor{\bsnm{Floor}, \binits{R.J.}},
\bauthor{\bsnm{Jekel}, \binits{P.A.}},
\bauthor{\bsnm{Baker}, \binits{D.}},
\bauthor{\bsnm{Marrink}, \binits{S.J.}},
\bauthor{\bsnm{Janssen}, \binits{D.B.}}:
\batitle{Computationally designed libraries for rapid enzyme stabilization}.
\bjtitle{Protein Engineering, Design and Selection}
\bvolume{27}(\bissue{2}),
\bfpage{49}--\blpage{58}
(\byear{2014})
\end{barticle}
\endbibitem

%%% 13
\bibitem{crooks2004weblogo}
\begin{barticle}
\bauthor{\bsnm{Crooks}, \binits{G.E.}},
\bauthor{\bsnm{Hon}, \binits{G.}},
\bauthor{\bsnm{Chandonia}, \binits{J.-M.}},
\bauthor{\bsnm{Brenner}, \binits{S.E.}}:
\batitle{Weblogo: a sequence logo generator}.
\bjtitle{Genome research}
\bvolume{14}(\bissue{6}),
\bfpage{1188}--\blpage{1190}
(\byear{2004})
\end{barticle}
\endbibitem

%%% 14
\bibitem{schneider1990sequence}
\begin{barticle}
\bauthor{\bsnm{Schneider}, \binits{T.D.}},
\bauthor{\bsnm{Stephens}, \binits{R.M.}}:
\batitle{Sequence logos: a new way to display consensus sequences}.
\bjtitle{Nucleic acids research}
\bvolume{18}(\bissue{20}),
\bfpage{6097}--\blpage{6100}
(\byear{1990})
\end{barticle}
\endbibitem

%%% 15
\bibitem{Gutmann2010Noise}
\begin{barticle}
\bauthor{\bsnm{Gutmann}, \binits{M.}},
\bauthor{\bsnm{Hyv{\"a}rinen}, \binits{A.}}:
\batitle{Noise-contrastive estimation: A new estimation principle for
  unnormalized statistical models}.
\bjtitle{Journal of Machine Learning Research}
\bvolume{9},
\bfpage{297}--\blpage{304}
(\byear{2010})
\end{barticle}
\endbibitem

%%% 16
\bibitem{Kingma2014Adam}
\begin{botherref}
\oauthor{\bsnm{Kingma}, \binits{D.P.}},
\oauthor{\bsnm{Ba}, \binits{J.}}:
Adam: A method for stochastic optimization.
Computer Science
(2014)
\end{botherref}
\endbibitem

%%% 17
\bibitem{zhang2015model}
\begin{barticle}
\bauthor{\bsnm{Zhang}, \binits{X.}},
\bauthor{\bsnm{Zou}, \binits{G.}},
\bauthor{\bsnm{Carroll}, \binits{R.J.}}:
\batitle{Model averaging based on kullback-leibler distance}.
\bjtitle{Statistica Sinica}
\bvolume{25},
\bfpage{1583}
(\byear{2015})
\end{barticle}
\endbibitem

%%% 18
\bibitem{maaten2008visualizing}
\begin{barticle}
\bauthor{\bsnm{Maaten}, \binits{L.v.d.}},
\bauthor{\bsnm{Hinton}, \binits{G.}}:
\batitle{Visualizing data using t-sne}.
\bjtitle{Journal of machine learning research}
\bvolume{9}(\bissue{Nov}),
\bfpage{2579}--\blpage{2605}
(\byear{2008})
\end{barticle}
\endbibitem

%%% 19
\bibitem{chang2011libsvm}
\begin{barticle}
\bauthor{\bsnm{Chang}, \binits{C.-C.}},
\bauthor{\bsnm{Lin}, \binits{C.-J.}}:
\batitle{Libsvm: a library for support vector machines}.
\bjtitle{ACM transactions on intelligent systems and technology (TIST)}
\bvolume{2}(\bissue{3}),
\bfpage{27}
(\byear{2011})
\end{barticle}
\endbibitem

%%% 20
\bibitem{goodfellow2016deep}
\begin{bbook}
\bauthor{\bsnm{Goodfellow}, \binits{I.}},
\bauthor{\bsnm{Bengio}, \binits{Y.}},
\bauthor{\bsnm{Courville}, \binits{A.}}:
\bbtitle{Deep Learning}.
\bpublisher{MIT press}, \blocation{???}
(\byear{2016})
\end{bbook}
\endbibitem

%%% 21
\bibitem{ruller2014concommitant}
\begin{barticle}
\bauthor{\bsnm{Ruller}, \binits{R.}},
\bauthor{\bsnm{Alponti}, \binits{J.}},
\bauthor{\bsnm{Deliberto}, \binits{L.A.}},
\bauthor{\bsnm{Zanphorlin}, \binits{L.M.}},
\bauthor{\bsnm{Machado}, \binits{C.B.}},
\bauthor{\bsnm{Ward}, \binits{R.J.}}:
\batitle{Concommitant adaptation of a gh11 xylanase by directed evolution to
  create an alkali-tolerant/thermophilic enzyme}.
\bjtitle{Protein Engineering, Design \& Selection}
\bvolume{27}(\bissue{8}),
\bfpage{255}--\blpage{262}
(\byear{2014})
\end{barticle}
\endbibitem

\end{thebibliography}

\newcommand{\BMCxmlcomment}[1]{}

\BMCxmlcomment{

<refgrp>

<bibl id="B1">
  <title><p>Protein structure prediction from sequence variation</p></title>
  <aug>
    <au><snm>Marks</snm><fnm>DS</fnm></au>
    <au><snm>Hopf</snm><fnm>TA</fnm></au>
    <au><snm>Sander</snm><fnm>C</fnm></au>
  </aug>
  <source>Nature biotechnology</source>
  <publisher>Nature Publishing Group</publisher>
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  <volume>30</volume>
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</bibl>

<bibl id="B2">
  <title><p>GH11 xylanases: structure/function/properties relationships and
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  <aug>
    <au><snm>Pa{\"e}s</snm><fnm>G</fnm></au>
    <au><snm>Berrin</snm><fnm>JG</fnm></au>
    <au><snm>Beaugrand</snm><fnm>J</fnm></au>
  </aug>
  <source>Biotechnology advances</source>
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  <fpage>564</fpage>
  <lpage>-592</lpage>
</bibl>

<bibl id="B3">
  <title><p>Enhancement in catalytic activity of Aspergillus niger XynB by
  selective site-directed mutagenesis of active site amino acids</p></title>
  <aug>
    <au><snm>Wu</snm><fnm>X</fnm></au>
    <au><snm>Tian</snm><fnm>Z</fnm></au>
    <au><snm>Jiang</snm><fnm>X</fnm></au>
    <au><snm>Zhang</snm><fnm>Q</fnm></au>
    <au><snm>Wang</snm><fnm>L</fnm></au>
  </aug>
  <source>Applied microbiology and biotechnology</source>
  <publisher>Springer</publisher>
  <pubdate>2018</pubdate>
  <volume>102</volume>
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  <lpage>-260</lpage>
</bibl>

<bibl id="B4">
  <title><p>Prediction of thermophilic proteins using feature selection
  technique</p></title>
  <aug>
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    <au><snm>Chen</snm><fnm>W</fnm></au>
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  <source>Journal of microbiological methods</source>
  <publisher>Elsevier</publisher>
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  <lpage>-70</lpage>
</bibl>

<bibl id="B5">
  <title><p>The hydrophobic temperature dependence of amino acids directly
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    <au><snm>Hoogeveen</snm><fnm>A</fnm></au>
    <au><snm>Abeln</snm><fnm>S</fnm></au>
  </aug>
  <source>PLoS computational biology</source>
  <publisher>Public Library of Science</publisher>
  <pubdate>2015</pubdate>
  <volume>11</volume>
  <issue>5</issue>
  <fpage>e1004277</fpage>
</bibl>

<bibl id="B6">
  <title><p>Stability curve prediction of homologous proteins using
  temperature-dependent statistical potentials</p></title>
  <aug>
    <au><snm>Pucci</snm><fnm>F</fnm></au>
    <au><snm>Rooman</snm><fnm>M</fnm></au>
  </aug>
  <source>PLoS computational biology</source>
  <publisher>Public Library of Science</publisher>
  <pubdate>2014</pubdate>
  <volume>10</volume>
  <issue>7</issue>
  <fpage>e1003689</fpage>
</bibl>

<bibl id="B7">
  <title><p>SCooP: an accurate and fast predictor of protein stability curves
  as a function of temperature</p></title>
  <aug>
    <au><snm>Pucci</snm><fnm>F</fnm></au>
    <au><snm>Kwasigroch</snm><fnm>JM</fnm></au>
    <au><snm>Rooman</snm><fnm>M</fnm></au>
  </aug>
  <source>Bioinformatics</source>
  <publisher>Oxford University Press</publisher>
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  <issue>21</issue>
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</bibl>

<bibl id="B8">
  <title><p>Recent advances in sequence-based protein structure
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    <au><snm>Kc</snm><fnm>DB</fnm></au>
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  <source>Briefings in bioinformatics</source>
  <publisher>Oxford University Press</publisher>
  <pubdate>2016</pubdate>
  <volume>18</volume>
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  <fpage>1021</fpage>
  <lpage>-1032</lpage>
</bibl>

<bibl id="B9">
  <title><p>Importance of improving scoring methods in predicting protein
  free-energy changes</p></title>
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    <au><snm>Liu</snm><fnm>S</fnm></au>
  </aug>
  <pubdate>2012</pubdate>
  <fpage>600</fpage>
  <lpage>-603</lpage>
</bibl>

<bibl id="B10">
  <title><p>Prediction of protein stability changes upon one-point mutations
  using machine learning</p></title>
  <aug>
    <au><snm>Malinka</snm><fnm>F</fnm></au>
  </aug>
  <source>Proceedings of the 2015 Conference on research in adaptive and
  convergent systems</source>
  <pubdate>2015</pubdate>
  <fpage>102</fpage>
  <lpage>-107</lpage>
</bibl>

<bibl id="B11">
  <title><p>PoPMuSiC 2.1: a web server for the estimation of protein stability
  changes upon mutation and sequence optimality</p></title>
  <aug>
    <au><snm>Dehouck</snm><fnm>Y</fnm></au>
    <au><snm>Kwasigroch</snm><fnm>JM</fnm></au>
    <au><snm>Gilis</snm><fnm>D</fnm></au>
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  </aug>
  <source>BMC bioinformatics</source>
  <publisher>BioMed Central</publisher>
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</bibl>

<bibl id="B12">
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    <au><snm>Baker</snm><fnm>D</fnm></au>
    <au><snm>Marrink</snm><fnm>SJ</fnm></au>
    <au><snm>Janssen</snm><fnm>DB</fnm></au>
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</bibl>

<bibl id="B13">
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    <au><snm>Chandonia</snm><fnm>JM</fnm></au>
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<bibl id="B14">
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<bibl id="B15">
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    <au><snm>Gutmann</snm><fnm>M</fnm></au>
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<bibl id="B16">
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<bibl id="B17">
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<bibl id="B18">
  <title><p>Visualizing data using t-SNE</p></title>
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</refgrp>
} % end of \BMCxmlcomment
