FLEXOME software suite
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 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.
Cite this dataset as:
Wells, S.,
2023.
FLEXOME software suite.
Version 2.
Bath: University of Bath Research Data Archive.
Available from: https://doi.org/10.15125/BATH-00995.
Export
Access on request: 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 access to the suite on condition that they agree to our assertion of rights, as set out in the file RIGHTS.txt.
Creators
Stephen Wells
University of Bath
Contributors
University of Bath
Rights Holder
Documentation
Data collection method:
C++ code written by Dr. Stephen A Wells, University of Bath, 2020–23.
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:
Source code in the form of C++ files (.h and .cpp) is in the CPP/ directory. Useful ancillary scripts written for Bash, PyMOL and the expert systems in FLEXOME 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.
Documentation Files
RIGHTS.txt
text/plain (1kB)
All Rights Reserved
Assertion of rights
Funders
Self-funded
Publication details
Publication date: 26 September 2023
by: University of Bath
Version: 2
This is the latest version of this item.
- Version 1. (23 November 2020)
- Version 2. (26 September 2023) [Currently Displayed]
DOI: https://doi.org/10.15125/BATH-00995
URL for this record: https://researchdata.bath.ac.uk/id/eprint/995
Related papers and books
Noby, N., Auhim, H. S., Winter, S., Worthy, H. L., Embaby, A. M., Saeed, H., Hussein, A., Pudney, C. R., Rizkallah, P. J., Wells, S. A., and Jones, D. D., 2021. Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism. Open Biology, 11(12). Available from: https://doi.org/10.1098/rsob.210182.
Elder, F. C. T., Pascoe, B., Wells, S., Sheppard, S. K., Snape, J., Gaze, W. H., Feil, E. J., and Kasprzyk-Hordern, B., 2022. Stereoselective metabolism of chloramphenicol by bacteria isolated from wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics. Water Research, 217, 118415. Available from: https://doi.org/10.1016/j.watres.2022.118415.
Ramakrishnan, K., Johnson, R. L., Winter, S. D., Worthy, H. L., Thomas, C., Humer, D. C., Spadiut, O., Hindson, S. H., Wells, S., Barratt, A. H., Menzies, G. E., Pudney, C. R., and Jones, D. D., 2023. Glycosylation increases active site rigidity leading to improved enzyme stability and turnover. The FEBS Journal, 290(15), 3812-3827. Available from: https://doi.org/10.1111/febs.16783.
Contact information
Please contact the Research Data Service in the first instance for all matters concerning this item.
Contact person: Stephen Wells
Faculty of Engineering & Design
Chemical Engineering
Faculty of Science
Chemistry
