FLEXOME software suite, first release 23/11/2020

Dataset

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.
Date made available23 Nov 2020
PublisherUniversity of Bath

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