FLEXOME software suite, first release 23/11/2020

This protein analysis software identifies rigid and flexible regions in a protein crystal structure; identifies easy directions of motion for the structure; and explores the motion of the structure along these directions. This generates a set of flexible variations on the starting structure, suggestive of the range of variation it will explore naturally in solution.

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.

Keywords:
FLEXOME, protein rigidity analysis, protein normal mode analysis, elastic network modelling, pebble game, geometric simulation, flexible motion, protein flexibility, protein software
Subjects:
Biomolecules and biochemistry

Cite this dataset as:
Wells, S., 2020. FLEXOME software suite, first release 23/11/2020. Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-00940.

Export

[QR code for this page]

Access restrictions apply: This dataset consists of a software suite which we expect to be of interest to both academic and commercial (biopharma) users. Users applying from a valid academic email address should be permitted to download the suite provided that they have agreed to our assertion of rights, as follows: RIGHTS The program is not to be distributed to anyone else without the express permission of the author ‚Äčor the University of Bath. All rights in the code and the algorithms used in the program remain with the University of Bath and the author. The program is not to be used for commercial research. For any commercial use of the program a license must be obtained from the University of Bath, including contract research. Commercial contact should be made at: research-commercialisation@bath.ac.uk The program is supplied on an "as is" basis with no implied guarantee or support. No warranty is expressed or implied. Neither the University of Bath nor the author shall under any circumstances be responsible or liable for any loss, damage, costs or other liability whatsoever which the user may incur as a result of using the program. The rights asserted apply to the entire contents of this distribution, whether or not they are explicitly repeated in a particular subdirectory or file of this distribution.

Creators

Documentation

Data collection method:

C++ code written by Dr. Stephen A Wells, University of Bath, 2020.

Technical details and requirements:

The code was written, and should be run, in a Linux command-line environment. The development environment was Cygwin on a Windows laptop with the gcc compiler. Shell scripts are written for the Bash shell. PyMOL scripts are provided to aid visualisation.

Additional information:

All code and compilation scripts are in the CPP/ directory. Detailed usage, user manual, and worked example are in the HOWTO/ directory.

Funders

Self-funded

Publication details

Publication date: 23 November 2020
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-00940

URL for this record: https://researchdata.bath.ac.uk/id/eprint/940

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Stephen A. Wells

Departments:

Faculty of Engineering & Design
Chemical Engineering

Faculty of Science
Chemistry