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                                "uri": "http://edamontology.org/data_1026",
                                "term": "Gene symbol"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3475",
                                    "term": "TSV"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1254",
                                "term": "Sequence property"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3475",
                                    "term": "TSV"
                                }
                            ]
                        }
                    ],
                    "note": "AIRR compatible V-J gene calling",
                    "cmd": "python DeRR.py [OPTIONS]"
                }
            ],
            "toolType": [
                "Script",
                "Command-line tool"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3930",
                    "term": "Immunogenetics"
                }
            ],
            "operatingSystem": [],
            "language": [
                "Python"
            ],
            "license": null,
            "collectionID": [],
            "maturity": "Mature",
            "cost": "Free of charge (with restrictions)",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/GuoBioinfoLab/DeRR",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://github.com/GuoBioinfoLab/DeRR",
                    "type": "Source code",
                    "note": null,
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "https://github.com/GuoBioinfoLab/DeRR/blob/main/README.md",
                    "type": [
                        "Quick start guide"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/gpbjnl/qzaf090",
                    "pmid": "41051256",
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": null
                }
            ],
            "credit": [
                {
                    "name": "Anyuan Guo",
                    "email": "guoanyuan@wchscu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "owner": "laupaard",
            "additionDate": "2026-06-12T12:35:12.904681Z",
            "lastUpdate": "2026-06-12T13:26:08.934404Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "ProteinsPlus",
            "description": "The ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.",
            "homepage": "https://proteins.plus",
            "biotoolsID": "proteinsplus",
            "biotoolsCURIE": "biotools:proteinsplus",
            "version": [],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "dogsitescorer",
                    "type": "includes"
                },
                {
                    "biotoolsID": "dogsite3",
                    "type": "includes"
                },
                {
                    "biotoolsID": "edia",
                    "type": "includes"
                },
                {
                    "biotoolsID": "siena",
                    "type": "includes"
                },
                {
                    "biotoolsID": "metalizer",
                    "type": "includes"
                },
                {
                    "biotoolsID": "structureprofiler",
                    "type": "includes"
                },
                {
                    "biotoolsID": "jamda",
                    "type": "includes"
                },
                {
                    "biotoolsID": "geomine",
                    "type": "includes"
                },
                {
                    "biotoolsID": "microminer",
                    "type": "includes"
                },
                {
                    "biotoolsID": "poseedit",
                    "type": "includes"
                },
                {
                    "biotoolsID": "poseview",
                    "type": "includes"
                },
                {
                    "biotoolsID": "protoss",
                    "type": "includes"
                },
                {
                    "biotoolsID": "lifesoaks",
                    "type": "includes"
                },
                {
                    "biotoolsID": "ppi",
                    "type": "includes"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0394",
                            "term": "Hydrogen bond calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3021",
                                "term": "UniProt accession"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "note": "prediction of protonation states and tautomers and placement of hydrogen atoms",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0321",
                            "term": "Protein structure validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2406",
                            "term": "Protein structure analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3695",
                            "term": "Data filtering"
                        },
                        {
                            "uri": "http://edamontology.org/operation_1844",
                            "term": "Protein geometry validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1539",
                                "term": "Protein structural quality report"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2991",
                                "term": "Protein geometry data"
                            },
                            "format": []
                        }
                    ],
                    "note": "quality profiling for protein-ligand complexes",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0570",
                            "term": "Structure visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0384",
                            "term": "Accessible surface calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2480",
                            "term": "Structure analysis"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1537",
                                "term": "Protein structure report"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2019",
                                "term": "Map data"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1542",
                                "term": "Protein solvent accessibility"
                            },
                            "format": []
                        }
                    ],
                    "note": "calculating bottleneck radii for crystal solvent channels",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0321",
                            "term": "Protein structure validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0570",
                            "term": "Structure visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3695",
                            "term": "Data filtering"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1772",
                                "term": "Score"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1537",
                                "term": "Protein structure report"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2019",
                                "term": "Map data"
                            },
                            "format": []
                        }
                    ],
                    "note": "atom-level assessment of the electron density fit for structures solved by X-ray crystallography",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2949",
                            "term": "Protein-protein interaction analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2406",
                            "term": "Protein structure analysis"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1772",
                                "term": "Score"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "note": "protein-protein interface classification (permanent, transient, crystal artifact)",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0394",
                            "term": "Hydrogen bond calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_1839",
                            "term": "Salt bridge calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0248",
                            "term": "Residue interaction calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0482",
                            "term": "Protein-ligand docking"
                        },
                        {
                            "uri": "http://edamontology.org/operation_1834",
                            "term": "Protein-metal contact calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
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                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1461",
                                "term": "Protein-ligand complex"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3021",
                                "term": "UniProt accession"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1197",
                                    "term": "InChI"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1196",
                                    "term": "SMILES"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3816",
                                    "term": "Mol2"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1537",
                                "term": "Protein structure report"
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                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
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                            ]
                        },
                        {
                            "data": {
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                                "term": "Protein-ligand complex"
                            },
                            "format": [
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                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1772",
                                "term": "Score"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3814",
                                    "term": "SDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1497",
                                "term": "Root-mean-square deviation"
                            },
                            "format": []
                        }
                    ],
                    "note": "protein-ligand docking for small molecules",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2406",
                            "term": "Protein structure analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3897",
                            "term": "Ligand-binding site prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
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                            "format": [
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                                    "uri": "http://edamontology.org/format_1476",
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                        {
                            "data": {
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                                "term": "Protein-ligand complex"
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                                    "term": "SDF"
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                            ]
                        },
                        {
                            "data": {
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                            "format": []
                        },
                        {
                            "data": {
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                                "term": "Small molecule structure"
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                            ]
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                    ],
                    "output": [
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                            "data": {
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                                "term": "Protein features"
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                                    "uri": "http://edamontology.org/format_2330",
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                        },
                        {
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