{"id":21629392,"url":"https://github.com/khanovico/neural-struct-detect","last_synced_at":"2026-02-27T16:41:22.302Z","repository":{"id":246010267,"uuid":"817290993","full_name":"khanovico/neural-struct-detect","owner":"khanovico","description":"deep neural network for detecting structure of protein","archived":false,"fork":false,"pushed_at":"2024-06-26T18:23:47.000Z","size":33303,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-05T08:41:47.635Z","etag":null,"topics":["artificial-intelligence","biological-data-analysis","deep-learning","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/khanovico.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-06-19T12:01:55.000Z","updated_at":"2024-06-30T16:19:55.000Z","dependencies_parsed_at":"2024-06-26T22:45:17.683Z","dependency_job_id":null,"html_url":"https://github.com/khanovico/neural-struct-detect","commit_stats":null,"previous_names":["khanovict/deep-tough","khanovict/neural-struct-detect","xleonsalman/neural-struct-detect","khanovico/neural-struct-detect"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanovico%2Fneural-struct-detect","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanovico%2Fneural-struct-detect/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanovico%2Fneural-struct-detect/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/khanovico%2Fneural-struct-detect/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/khanovico","download_url":"https://codeload.github.com/khanovico/neural-struct-detect/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240356060,"owners_count":19788512,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["artificial-intelligence","biological-data-analysis","deep-learning","python"],"created_at":"2024-11-25T02:07:36.861Z","updated_at":"2026-02-27T16:41:17.257Z","avatar_url":"https://github.com/khanovico.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Deep Nerual Network approach for Sturcture Detection\n\n## Setup\n\nThe software is ready for Docker: the image can be created from `Dockerfile` by running `docker build -t deeplytough .` (image size ~4.7GB so you may have to increase the disk space available to docker). The DeeplyTough tool is then accessible\nconda environment inside the container with `source activate deeplytough`.\n\n```bash\n# create new python 3 env and activate\nconda create -y -n deeplytough python=3.6\n# create python2 env used for protein structure preprocessing\nconda create -y -n deeplytough_mgltools python=2.7\nconda install -y -n deeplytough_mgltools -c bioconda mgltools=1.5.6\n```\n### Environment setup\n\nTo run the evaluation and training scripts, please first set the `DEEPLYTOUGH` environment variable to the directory containing this repository and then update the `PYTHONPATH` and `PATH` variables respectively:\n```bash\nexport DEEPLYTOUGH=/path_to_this_repository\nexport PYTHONPATH=$DEEPLYTOUGH/deeplytough:$PYTHONPATH\nexport PATH=$DEEPLYTOUGH/fpocket2/bin:$PATH\n```\n\n## Training\n\nTraining requires a GPU with \u003e=11GB of memory and takes about 1.5 days on recent hardware. In addition, at least a 4-core CPU is recommended due to volumetric input pre-processing being an expensive task.\n\nNote that due to non-determinism inherent to the currently established process of training deep networks, it is nearly impossible to exactly reproduce the pre-trained networks in `networks` directory.\n\nAlso note the convenience of an output directory containing \"TTTT\" will afford this substring being replaced by the current `datetime`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanovico%2Fneural-struct-detect","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkhanovico%2Fneural-struct-detect","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanovico%2Fneural-struct-detect/lists"}