OpenCDSurf

OpenCDSurf is an open-source software which computes cavity accessibility in cyclodextrin (CD) derivatives. OpenCDSurf was developed with the aim of processing the output of a molecular dynamics (MD) trajectory, previously converted into a collection of PDB files. The program automatically identifies each individual CD in the PDB file, no matter whether it is alone, derivatized or included in macromolecular adducts, and computes the solvent accessible surface of its cavity. To accomplish this task, each CD cavity is first filled with oxygen atoms; subsequently, the EDTSurf algorithm developed in the Zhang Lab is invoked, which computes the solvent accessible surface (SAS) of these atoms, keeping into account other atoms eventually present in the environment which may hinder the access to the cavity, e.g. the atoms of the sugar monomers themselves, or other moieties which may be connected to the CD core. OpenCDSurf is controlled through a command line interface; detailed instructions for use may be found here. The output consists of a list of the computed surface areas in Ų for each individual CD. Additionally, a PDB file can be obtained which includes the atoms used to fill the CD cavities, in order to enable visualization of the SAS with a 3D molecular modelling package such as MOE or PyMOL. OpenCDSurf is written in C++; while pre-built binaries are available for mainstream operating systems (Windows, Linux, Solaris x86, FreeBSD, Intel Mac OS X), source code is portable and can be compiled under any *NIX platform. The modular nature of the code allows for easy implementation of new features, so that the core application can be customized to meet individual needs. A ChangeLog is kept to keep track of the additions and modifications during OpenCDSurf's development.