\babel@toc {english}{}\relax 
\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
\contentsline {chapter}{\numberline {3}Analyzing and Modifying the ESCOTT Output}{9}{chapter.3}%
\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}%
\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}%
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
\contentsline {chapter}{\numberline {5}Installation}{13}{chapter.5}%
\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}%
\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}%
\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}%
\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}%
