FLEXOME software suite, first release 23/11/2020

940 42 13704 2 42962 document 13704 FLEXOME23112020.zip application/zip b0e0634748d7f6ede532ba22f293ba7e MD5 62971871 2020-11-23 14:33:21 https://researchdata.bath.ac.uk/940/1/FLEXOME23112020.zip 940 1 1 application/zip other Code, documentation and examples for the "FLEXOME" software suite, written by Stephen A. Wells at the University of Bath, 2020. This suite carries out rigidity analysis, normal mode analysis and geometric simulations of flexible motion in protein structures. This deposition is intended as a means of providing the code to academic users by request, subject to our conditions as follows: RIGHTS The program is not to be distributed to anyone else without the express permission of the author or en staffonly all_rights_reserved

FLEXOME23112020.zip

code 13705 2 42965 document 13705 README.txt text/plain 235fae817130b3019987e7dba7f6cc1c MD5 1167 2020-11-23 15:03:50 https://researchdata.bath.ac.uk/940/2/README.txt 940 2 2 text/plain other Summary README from topmost directory. en staffonly all_rights_reserved

README.txt

documentation 13706 2 42967 document 13706 USAGE.txt text/plain aa9b03d22fce3d710ca3e1e531142b12 MD5 3509 2020-11-23 15:04:45 https://researchdata.bath.ac.uk/940/3/USAGE.txt 940 3 3 text/plain other Usage information for all executables in the suite. en staffonly all_rights_reserved

USAGE.txt

documentation 13707 2 42969 document 13707 FLEXOME-GUIDANCE.txt text/plain 182fca6ecb26fcb22bc371a49d958b85 MD5 29232 2020-11-23 15:05:23 https://researchdata.bath.ac.uk/940/4/FLEXOME-GUIDANCE.txt 940 4 4 text/plain other Detailed user manual describing code compilation and usage. en staffonly all_rights_reserved

FLEXOME-GUIDANCE.txt

documentation 13708 2 42976 document 13708 Dataplan.txt text/plain b06e70a5726c84c22b8c548bbd47b3ec MD5 784 2020-11-23 15:24:34 https://researchdata.bath.ac.uk/940/5/Dataplan.txt 940 5 5 text/plain other Precis of code development and intention for deposition and request handling. en staffonly all_rights_reserved

Dataplan.txt

dmp 13709 1 42980 document 13709 indexcodes.txt text/plain 6fc10471a82d053e58ded8088c205c33 MD5 610 2020-11-23 15:25:33 https://researchdata.bath.ac.uk/940/6/indexcodes.txt 940 6 6 text/plain other Generate index codes conversion from other to indexcodes en staffonly

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/13705 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/13705 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/13705 13710 1 42981 document 13710 indexcodes.txt text/plain 14c4a1ef793351c31c0329441fd9338a MD5 1193 2020-11-23 15:25:33 https://researchdata.bath.ac.uk/940/7/indexcodes.txt 940 7 7 text/plain other Generate index codes conversion from other to indexcodes en staffonly

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/13706 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/13706 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/13706 13711 1 42982 document 13711 indexcodes.txt text/plain 321690c2f8ccf2e5f72bee16e3034238 MD5 6388 2020-11-23 15:25:33 https://researchdata.bath.ac.uk/940/8/indexcodes.txt 940 8 8 text/plain other Generate index codes conversion from other to indexcodes en staffonly

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/13707 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/13707 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/13707 13712 1 42983 document 13712 indexcodes.txt text/plain 24dda380cc438509bc91cf45d35984af MD5 451 2020-11-23 15:25:33 https://researchdata.bath.ac.uk/940/9/indexcodes.txt 940 9 9 text/plain other Generate index codes conversion from other to indexcodes en staffonly

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/13708 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/13708 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/13708 14560 2 45364 document 14560 RIGHTS.txt text/plain e39877b5db20f36785196c34dcbc4dc5 MD5 1105 2021-03-01 09:46:36 https://researchdata.bath.ac.uk/940/10/RIGHTS.txt 940 10 10 text/plain other Assertion of rights en public all_rights_reserved

RIGHTS.txt

documentation 14561 1 45366 document 14561 indexcodes.txt text/plain b39758b7229349da869b637e0e5d8062 MD5 591 2021-03-01 09:47:06 https://researchdata.bath.ac.uk/940/11/indexcodes.txt 940 11 11 text/plain other Generate index codes conversion from other to indexcodes en public

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/14560 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/14560 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/14560 archive 4129 disk0/00/00/09/40 2020-11-25 15:46:28 2024-05-14 13:12:09 2021-03-01 09:50:19 data_collection no_search Wells Stephen S.A.Wells@bath.ac.uk 0000-0002-3920-3644 University of Bath TRUE FLEXOME software suite, first release 23/11/2020 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 All code and compilation scripts are in the CPP/ directory. Detailed usage, user manual, and worked example are in the HOWTO/ directory. 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. 2020-11-23 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. 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 1 10.15125/BATH-00940 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