\babel@toc {english}{}
\contentsline {chapter}{\numberline {1}Using ESGEMME via Docker}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}Requirements}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}%
\contentsline {section}{\numberline {1.3}Single point mutation calculations}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Obtaining the entire single point mutation landscape}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Predicting the effect of a subset of single point mutations}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Multiple point mutation calculations}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Analyzing and Modifying the ESGEMME Output}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Raw ESGEMME Scores and Their Interpretation}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}%
\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}%
\contentsline {section}{\numberline {3.1}Preparing Your Input MSA and PDB with Colabfold}{7}{section.3.1}%
\contentsline {chapter}{\numberline {4}Installation}{9}{chapter.4}%
\contentsline {section}{\numberline {4.1}Installing the dependencies:}{9}{section.4.1}%
\contentsline {section}{\numberline {4.2}Getting the source code and preparing the environment:}{9}{section.4.2}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{9}{section.4.3}%
\contentsline {chapter}{\numberline {5}Indices and tables}{11}{chapter.5}%
