name: 'Dynabench: Dynamic data for the docking benchmark; 3HI6'
description: 'The Dynabench database provides all-atom Molecular Dynamics (MD) trajectories for the protein-protein complexes from the Docking Benchmark (DB) v. 5.5 (Guest et al. Structure 2021), which comprises over 200 non-redundant protein assemblies distributed over different functional groups (Enzyme/Inhibitor, Antibody/Antigen and others) and three difficulty groups regarding the amplitude of the conformational changes undergone by the protein partners upon binding.'
authors:
    - 'Sophie Sacquin-Mora'
    - 'Chantal Prévost'
    - 'Ezgi Karaca'
    - 'Ayşe Berçin Barlas'
    - 'Benoist Laurent'
groups:
    - 'Université Paris-Cité et CNRS UMR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France'
    - 'Computational Structural Biology Lab (CSB), Izmir Biomedicine and Genome Center, Turkey'
contact: sacquin@ibcp.fr
program: NAMD
version: '2.13'
type: trajectory
method: 'Classical MD'
license: null
linkcense: null
citation: null
thanks: 'HPC resources from GENCI-TGCC (grant A0120713385)'
accession: A00L6
links:
    -
        name: 'Protein-Protein Docking Benchmark 5.5'
        url: 'https://zlab.wenglab.org/benchmark/'
pdb_ids:
    - 3HI6
framestep: 0.1
temp: 300
ensemble: NPT
timestep: 2
ff:
    - CHARMM36m
wat: TIP3P
boxtype: Cubic
interactions:
    -
        name: 'chain B-chain F interaction'
        agent_1: 'chain B'
        agent_2: 'chain F'
        selection_1: 'chain B'
        selection_2: 'chain F'
    -
        name: 'chain D-chain F interaction'
        agent_1: 'chain D'
        agent_2: 'chain F'
        selection_1: 'chain D'
        selection_2: 'chain F'
pbc_selection: null
cg_selection: null
forced_references: null
multimeric: null
chainnames: null
ligands: null
membranes: null
customs: null
orientation: null
collections:
    - dynabench
mds:
    -
        name: 'replica 1/3, 100 ns'
        metadata:
            TEMP: 300
        directory: 'replica_1/3, 100 ns'
        input_structure_filepath: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.1/files/structure.pdb'
        input_trajectory_filepaths: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.1/files/trajectory.xtc'
    -
        name: 'replica 2/3, 100 ns'
        metadata:
            TEMP: 300
        directory: 'replica_2/3, 100 ns'
        input_structure_filepath: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.2/files/structure.pdb'
        input_trajectory_filepaths: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.2/files/trajectory.xtc'
    -
        name: 'replica 3/3, 100 ns'
        metadata:
            TEMP: 300
        directory: 'replica_3/3, 100 ns'
        input_structure_filepath: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.3/files/structure.pdb'
        input_trajectory_filepaths: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1.3/files/trajectory.xtc'
mdref: 0
input_topology_filepath: 'https://inria.mddbr.eu/api/rest/current/projects/A00L6.1/files/topology.psf'