Description
This dataset primarily contains 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.
Source code in the form of C++ files (.h and .cpp) is in the CPP/ directory. Useful ancillary scripts are in the SCRIPTS/ directory. The HOWTO/ directory includes a detailed user manual, "FLEXOME-GUIDANCE.txt"; a fully worked example, discussed in the manual, in the LysosymeExample/ directory; and an ExpertExample/ directory showing advanced FLEXOME usage options. Each directory includes a README.txt file summarising its contents and significance.
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.
Source code in the form of C++ files (.h and .cpp) is in the CPP/ directory. Useful ancillary scripts are in the SCRIPTS/ directory. The HOWTO/ directory includes a detailed user manual, "FLEXOME-GUIDANCE.txt"; a fully worked example, discussed in the manual, in the LysosymeExample/ directory; and an ExpertExample/ directory showing advanced FLEXOME usage options. Each directory includes a README.txt file summarising its contents and significance.
| Date made available | 23 Nov 2020 |
|---|---|
| Publisher | University of Bath |