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Contents.m
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Contents.m
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% PROMPT Toolbox
% Version 1.0 15-Dec-2014
%
% PROMPT (PRotein cOnformation Motion PredicTion) toolbox contains a set
% of functions to create and process coarse-grained models of protein
% conformational motion. The method implemented in the toolbox is described
% in the following paper.
%
% Modeling of Conformation Change by Redox-Switch Modulation of Human
% Succinic Semialdehyde Dehydrogenase by Gaik Tamazian, Jeong Ho Chang,
% Sergey Knyazev, Eugene Stepanov, Kyung-Jin Kim and Yuri Porozov.
% Submitted to PLoS Computational Biology journal.
%
% Demos
% calmodulin_demo - Calmodulin conformational motion simulation demo
%
% Functions
% atomicmass - Get atomic masses
% circdist - Calculate circular distance between angles
% circinterp - Circular interpolation of angles by the specified arcs
% createmodel - Get transformation bond lengths, planar and torsion angles
% cross3d - Simplified evalulation of a vector cross product for 3D vectors
% getbinarycode - Generate binary numbers from 0 to 2^N
% pdb2aa - Return a cell array of PDB structure amino acid sequences
% pdb2trm - Create a transformation model from a PDB structure
% pdbbackbone - Return a PDB structure only with backbone atoms
% pdbextractcoords - Extract Cartesian atom coordinates from a PDB structure
% pdbmininteratomicdist - Returns minimal interatomic distances
% pdbplotadjrmsd - Plot RMSDs between adjacent models
% pdbplotfixedrmsd - Plot RMSDs between models and the specified one
% pdbtrfcmp - Compare transformations from PDB structures
% pdbtrfcost - Calculate transformation cost from a PDB structure
% reduceangles - Reduce angular values to the interval [-pi, pi]
% restorecoords - Restore Cartesian coordinates of atoms
% sidechainmass - Get atomic masses of protein side chains
% sievefit - Apply the sieve-fit procedure to fit Y to X
% trm2pdb - Convert a transformation model to a PDB structure object
% trmcost - Calculate transformation cost
% trmcreate - Create a transformation model
% trmdistantangleindices - Get indices of the most distant torsion angles
% trmmininteratomicdist - Get minimal interatomic distances
% trmobjfunc - Calculate the cost function and its gradient for the model
% trmplotadjrmsd - Plot RMSDs between adjacent configurations
% trmplotfixedrmsd - Plot RMSDs between configurations and the specified one
% trmplottranglediff - Plot differences between transformation torsion angles
% trmrestorecoords - Restore Cartesian coordinates of transformation atoms
% trmupdaterotations - Update rotation matrices by the optimal superposition
% trmvariateinterpolations - Vary interpolation modes for torsion angles