995 27 14828 3 46205 document 14828 README.txt text/plain 235fae817130b3019987e7dba7f6cc1c MD5 1167 2020-11-23 15:03:50 https://researchdata.bath.ac.uk/995/2/README.txt 995 2 2 text/plain other Summary README from topmost directory. en staffonly all_rights_reserved

README.txt

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USAGE.txt

documentation 14830 3 46207 document 14830 FLEXOME-GUIDANCE.txt text/plain 182fca6ecb26fcb22bc371a49d958b85 MD5 29232 2020-11-23 15:05:23 https://researchdata.bath.ac.uk/995/4/FLEXOME-GUIDANCE.txt 995 4 4 text/plain other Detailed user manual describing code compilation and usage. en staffonly all_rights_reserved

FLEXOME-GUIDANCE.txt

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Dataplan.txt

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RIGHTS.txt

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ForDistributionV2.zip

code archive 4129 disk0/00/00/09/95 2023-09-26 12:21:34 2025-12-09 10:37:52 2023-09-26 12:21:34 data_collection 940 show Wells Stephen S.A.Wells@bath.ac.uk 0000-0002-3920-3644 University of Bath TRUE BY0050 BY0130 dept_chem_eng dept_chem FLEXOME, protein rigidity analysis, protein normal mode analysis, elastic network modelling, pebble game, geometric simulation, flexible motion, protein flexibility, protein software 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. 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. 2023-09-26 University of Bath restricted 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. RightsHolder University of Bath Self-funded C++ code written by Dr. Stephen A Wells, University of Bath, 2020–23. 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. en 2 10.15125/BATH-00995 https://doi.org/10.1098/rsob.210182 pub https://doi.org/10.1016/j.watres.2022.118415 pub https://doi.org/10.1111/febs.16783 pub 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. Software