SCREAM (Docker): The official version will be released soon (built with Rust)
SCREAM is a molecular modeling software package designed to accurately predict protein side-chain placements. Its core scientific contribution, as detailed in the JCTC 2008 paper (DOI: 10.1021/ct800196k - "Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements"), is the utilization of "flat-bottom" potentials for rotamer scoring. This strategy modifies the repulsive part of Van der Waals (VDW) and Hydrogen Bond (HB) potentials based on the coarseness of the rotamer library and specific atom types, allowing for greater tolerance in atomic contacts that arise from using discrete rotamer libraries. The project aims to improve the accuracy of computational protein structure prediction and design by providing a robust method for side-chain conformation determination.
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Timeline
feat(legacy): Initial import of legacy SCREAM source code
feat(docker): Add Dockerfile for CentOS 6 environment setup with Python 2.7 and development tools
feat(setup): Add installation script for SCREAM legacy Docker environment
feat(uninstall): Add uninstall script for SCREAM legacy environment
feat(script): Add scream-legacy script for executing SCREAM subcommands in Docker
fix(install): Correct image name in setup script to match Docker image
fix(uninstall): Update image name in uninstall script to match Docker image
fix(script): Update image name in scream script to match Docker image
feat(example): Add example script for executing SCREAM legacy commands
docs(readme): Add README for SCREAM Docker environment setup and usage
fix(example): Update output file extension in example script to .out
fix(readme): Update output file extension in usage example to .out
fix(readme): Correct formatting of SCREAM command in usage section
feat(script): Add help command to display available subcommands
feat(example): Add example script for ala scream execution
feat(example): Add example script for all scream execution
feat(example): Add example script for bindsite execution
fix(bindsite): Remove debug output from loadscream function
feat(example): Add example script for deala execution
feat(example): Add new example script for multi execution
docs(readme): Update usage example for scream-legacy command in README
docs(readme): Add license section to README
fix(readme): Update Python version to 2.7.18 in runtime section
