FLEXOME software suite

This dataset primarily contains C++ source code and instructions for a set of protein analysis utilities collectively called FLEXOME. FLEXOME can perform the following functions on a protein structure input:

- Identification of covalent, hydrophobic and polar interactions using the atomic geometry of the input.
- Surface exposure and burial distance finding.
- Rigid Cluster Decomposition using pebble-game rigidity analysis.
- Normal mode finding with an elastic network model, one site per residue. Only the requested number of low-frequency modes are generated, using Cholesky decomposition and inverse iteration, to avoid the computational cost of fully inverting a large matrix.
- Geometric simulations of flexible motion in the all-atom structure, using the input atomic geometry as constraints and a normal mode eigenvector as a bias direction.

The bond-detection routine has been updated since the originally committed version 1 for improved detection of metal-ion coordination by residues, which was not fully handled in the original version due to the omission of one of the checking loops. This version should correctly detect the coordination of, for example, iron by amide and carboxyl moieties in the protein.