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% This example file for NIH submissions was originally written
% by Bruce Donald (http://www.cs.duke.edu/brd/).
%
% You may freely use, modify and/or distribute this file.
%
\documentclass[11pt]{nih}
%\documentclass{article}
%\documentclass[12pt]{article}%
% last revision:
\def\mydate{2005-06-09 13:58:03 brd}
%%%%%%% Two column control
\newif\ifdotwocol
\dotwocoltrue % two col
%\dotwocolfalse % one col
\long\def\twocol#1#2{\ifdotwocol{#1}\else{#2}\fi}
%%%%%%%
\def\mybeforeequation{\footnotesize}
%\def\mybeforeequation{\small}
%\def\mybeforeequation{}
\def\myafterequation{\renewcommand\baselinestretch{1.1}}
%\def\myafterequation{}
%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%
\def\citeusmark{$^{\textstyle \star}$}
\def\citeus#1#2{\cite{#1}}
\def\crow#1#2{#2}
%\usepackage{denselists}
%\usepackage{scaledfullpage}
\usepackage[dvips]{graphicx}
\usepackage{color}
\usepackage{boxedminipage}
\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{url}
%\usepackage{times}
%\usepackage{nih} % PHS 398 Forms
%\usepackage{nihblank} % For printing on Blank PHS 398 Forms
%\usepackage{confidential}
\def\Paper{grant application}
\def\paper{application}
\def\refappendix{Sec.}
\def\poster{(Poster)}
%Note from brd
\long\def\todo#1{{\bf{To do:}} #1}
%\long\def\todo#1{}
\def\ICRA{IEEE International Conference on Robotics and Automation (ICRA)}
\long\def\squeezable#1{#1}
%\def\a5{$\alpha_{_5}$
\def\a5{5}
%\def\mycaptionsize{\normalsize}
%\def\mycaptionsize{\small}
%\def\mycaptionsize{\small}
\def\mycaptionsize{\footnotesize}
\def\mycodesize{\footnotesize}
\def\myeqnsize{\small}
\def\sheading#1{{\bf #1:}\ }
\def\sheading#1{\subsubsection{#1}}
%\def\sheading#1{\bigskip {\bf #1.}}
\def\ssheading#1{\noindent {\bf #1.}\ }
\newtheorem{hypothesis}{Hypothesis}
\long\def\hyp#1{\begin{hypothesis} #1 \end{hypothesis}}
\def\cbk#1{[{\em #1}]}
\def\R{\mathbb{R}}
\def\midv{\mathop{\,|\,}}
\def\Fscr{\mathcal{F}}
\def\Gscr{\mathcal{G}}
\def\Sscr{\mathcal{S}}
\def\set#1{{\{#1\}}}
\def\edge{\!\rightarrow\!}
\def\dedge{\!\leftrightarrow\!}
\newcommand{\EOP}{\nolinebreak[1]~~~\hspace*{\fill} $\Box$\vspace*{\parskip}\vspace*{1ex}}
%my way of doing starred references
\newcommand{\mybibitem}[1]{\bibitem{#1}
\label{mybiblabel:#1}}
\newcommand{\BC}{[}
\newcommand{\EC}{]}
\newcommand{\mycite}[1]{\ref{mybiblabel:#1}\nocite{#1}}
\newcommand{\starcite}[1]{\ref{mybiblabel:#1}\citeusmark\nocite{#1}}
\def\degree{$^\circ$}
\def\R{\mathbb{R}}
\def\Fscr{\mathcal{F}}
\def\set#1{{\{#1\}}}
\def\edge{\!\rightarrow\!}
\def\dedge{\!\leftrightarrow\!}
\long\def\gobble#1{}
\def\Jigsaw{{\sc Jigsaw}}
\def\ahelix{\ensuremath{\alpha}-helix}
\def\ahelices{\ensuremath{\alpha}-helices}
\def\ahelical{$\alpha$-helical}
\def\bstrand{\ensuremath{\beta}-strand}
\def\bstrands{\ensuremath{\beta}-strands}
\def\bsheet{\ensuremath{\beta}-sheet}
\def\bsheets{\ensuremath{\beta}-sheets}
\def\hone{{\ensuremath{^1}\rm{H}}}
\def\htwo{{$^{2}$H}}
\def\cthir{{\ensuremath{^{13}}\rm{C}}}
\def\nfif{{\ensuremath{^{15}}\rm{N}}}
\def\hn{{\rm{H}\ensuremath{^\mathrm{N}}}}
\def\hnone{{\textup{H}\ensuremath{^1_\mathrm{N}}}}
\def\ca{{\rm{C}\ensuremath{^\alpha}}}
\def\catwel{{\ensuremath{^{12}}\rm{C}\ensuremath{^\alpha}}}
\def\ha{{\rm{H}\ensuremath{^\alpha}}}
\def\cb{{\rm{C}\ensuremath{^\beta}}}
\def\hb{{\rm{H}\ensuremath{^\beta}}}
\def\hg{{\rm{H}\ensuremath{^\gamma}}}
\def\dnn{{\ensuremath{d_{\mathrm{NN}}}}}
\def\dan{{\ensuremath{d_{\alpha \mathrm{N}}}}}
\def\jconst{{\ensuremath{^{3}\mathrm{J}_{\mathrm{H}^{\mathrm{N}}\mathrm{H}^{\alpha}}}} }
\def\cbfb{{CBF-$\beta$}}
\newtheorem{defn}{Definition}
\newtheorem{claim}{Claim}
\gobble{
\psfrag{CO}[][]{\colorbox{white}{C}}
\psfrag{OO}[][]{\colorbox{white}{O}}
\psfrag{CA}[][]{\colorbox{white}{\ca}}
\psfrag{HA}[][]{\colorbox{white}{\ha}}
\psfrag{CB}[][]{\colorbox{white}{\cb}}
\psfrag{HB}[][]{\colorbox{white}{\hb}}
\psfrag{HN}[][]{\colorbox{white}{\hn}}
\psfrag{N15}[][]{\colorbox{white}{\nfif}}
\psfrag{dnn}[][]{\dnn}
\psfrag{dan}[][]{\dan}
\psfrag{phi}[][]{$\phi$}
}
\newenvironment{closeenumerate}{\begin{list}{\arabic{enumi}.}{\topsep=0in\itemsep=0in\parsep=0in\usecounter{enumi}}}{\end{list}}
\def\CR{\hspace{0pt}} % ``invisible'' space for line break
\newif\ifdbspacing
%\dbspacingtrue % For double spacing
\dbspacingfalse % For normal spacing
\ifdbspacing
\doublespacing
\newcommand{\capspacing}{\doublespace\mycaptionsize}
\else
\newcommand{\capspacing}{\mycaptionsize}
\fi
\def\rulefigure{\smallskip\hrule}
% \def\codesize{\normalsize}
\def\codesize{\small}
% Can use macros \be, \ee, \en as shortcuts
% for \begin{enumerate}, \end{enumerate}, \item
% respectively.
\def\be{\begin{enumerate}} % Begin Enumerate
\def\ee{\end{enumerate}} % End Enumerate
\def\en{\item} % ENtry (item)
\def\bi{\begin{itemize}} % Begin Itemize
\def\ei{\end{itemize}} % End Itemize
\def\bv{\begin{verbatim}} % Begin Verbatim
\def\ev{\end{verbatim}} % End Verbatim
\def\matlab{{\sc matlab} }
\def\amber{{\sc amber} }
\def\KS{{$K^*$}}
\def\KSM{{K^*}} % K-Star Math
\def\KSTM{{\tilde{K}^*}} % K-Star Tilde Math (appx K*)
\def\KOP{{$K^{\dagger}_{o}$}} % K-Star Optimal partial
\def\KOPM{{K^{\dagger}_{o}}} % K-Star Optimal partial Math
\def\KP{{$K^{\dagger}$}} % K-Star partial
\def\KPM{{K^{\dagger}}} % K-Star partial Math
\def\KTPM{{\tilde{K}^{\dagger}}} % K-Star Tilde partial Math
\def\KD{{$K_{_D}$}}
\def\KA{{$K_{_A}$}}
\def\qpM{{q_{_P}}}
\def\qlM{{q_{_L}}}
\def\qplM{{q_{_{PL}}}}
\def\qSplM{{q^*_{_{PL}}}}
\def\KSO{{$K^*_{o}$}} % K-Star Optimal
\def\KSOM{{K^*_{o}}} % K-Star Optimal Math
\def\CBFB{{CBF-$\beta$}} % Core binding factor beta
\def\argmin{\mathop{\mathrm{argmin}}}
\def\rhl#1{{\em \underline{RYAN}: *\{{#1}\}*}}
\def\set#1{{\left\{ #1 \right\}}}
\def\Escr{{\mathcal{E}}}
\def\Jscr{{\mathcal{J}}}
\def\Kscr{{\mathcal{K}}}
\def\th{{$^{{\mathrm{th}}}$}}
\newtheorem{proposition}{Proposition}
\newtheorem{lemma}{Lemma}
\begin{document}
\bigskip
\appendix
%\mydate
\setcounter{page}{20} % or whatever
%\noindent{\Large\bf Research Plan}
\section{Specific Aims}
\noindent Realization of novel molecular function requires the ability
to alter molecular complex formation. Enzymatic function can be
altered by changing enzyme-substrate interactions via modification of
an enzyme's active site. A redesigned enzyme may either perform a
novel reaction on its native substrates or its native reaction on
novel substrates. We propose a novel algorithm for protein redesign,
which searches over possible active site mutations and combines a
statistical mechanics-derived ensemble-based approach to computing the
binding constant with the speed and completeness of a branch-and-bound
pruning algorithm. We will develop an efficient$\ldots$
\end{document}
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