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605 simulations
Horizontal SoD COM-restrained +100 mV with prosECCo75 applied to all charged residues - replica 4
No authors listed
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-restraints and prosECCo75 applied to all charged residues (replica 4).
OpenNo structureCC BY 4.0Published 10 Oct 2026Horizontal SoD COM-unrestrained +100 mV with NBFIX - replica 4
No authors listed
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-unrestrained and NBFIX conditions (replica 4).
OpenNo structureCC BY 4.0Published 9 Oct 2026Horizontal SoD COM-unrestrained +100 mV with NBFIX - replica 3
No authors listed
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-unrestrained and NBFIX conditions (replica 3).
OpenNo structureCC BY 4.0Published 9 Oct 2026Horizontal SoD COM-restrained +100 mV with NBFIX - replica 1
No authors listed
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-restraints and NBFIX conditions (replica 1).
OpenNo structureCC BY 4.0Published 9 Oct 2026No description
OpenNo structurePublished 23 Jul 2026Structural redefinition of CTL1 as a membrane-remodelling phospholipid-binding protein; Membrane-embedded CTL1 monomer
Modesto Orozco
No description
OpenNo structurePublished 23 Jul 2026Structural redefinition of CTL1 as a membrane-remodelling phospholipid-binding protein; Membrane-embedded CTL1 dimer
Modesto Orozco
No description
OpenNo structurePublished 16 Jul 2026- No structurePublished 16 Jul 2026
- No structurePublished 16 Jul 2026
Coarse-grained simulation of TOC-P complex
No authors listed
Martini 2.2 Coarse-grained simulation of TOC-P complex: Toc33, Toc75, Toc159 embedded in a POPC membrane. TOC-P structures were generated from AF3 predictions in the webserver (https://alphafoldserver.com).
OpenNo structureCC BY 4.0Published 13 Mar 2026Mg2+-bound human oxytocin receptor bound to oxytocin
Francesco Musiani, Samira Al Sadi, Alejandro Giorgetti, et al.
Atomistic molecular dynamics simulations on the Mg2+-bound human oxytocin receptor bound to oxytocin in explicit solvent (physiological ionic strength) and membrane.
OpenPDB 7RYCPublished 6 Feb 2026Mg2+-bound human oxytocin receptor bound to oxytocin; system B
Francesco Musiani, Samira Al Sadi, Alejandro Giorgetti, et al.
Atomistic molecular dynamics simulations on the Mg2+-bound human oxytocin receptor bound to oxytocin in explicit solvent (physiological ionic strength) and membrane.
OpenPDB 7RYCPublished 10 Feb 2026Intrinsic dynamics of TARP gamma-2
James Krieger, Nayanika Sengupta, Alexander M. Scrutton, et al.
TARPs (transmembrane AMPA receptor regulatory proteins) are auxiliary subunits of AMPA-type glutamate receptors (AMPARs) that modulate receptor trafficking, gating, and pharmacology. Different TARPs bestow distinct functional properties on AMPARs, influencing synaptic transmission and plasticity. As part of a study on the Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum, we determined cryo-EM structures of native AMPARs in complex with TARPs, including GluA1/A4 heteromers with two TARPs, corresponding to the main Bergmann glia AMPAR. To help characterise these receptor complexes, the intrinsic dynamics of TARPs gamma-7 and gamma-2 in POPC membrane bilayer in the absence of the AMPAR was investigated using all-atom molecular dynamics simulations. Our simulations support gamma-7 as the main Bergmann glia TARP as they exhibit a straightening of transmembrane helix 2 (TM2) in 7 simulations, in line with a dominant cryo-EM class. By contrast, the well-studied TARP gamma-2 maintains a pronounced kink in TM2 characteristic of Type I TARPs for 100 ns in 3 simulations. Thus, MD simulations indicate that a straight TM2 is a hallmark of Type II TARPs with the previously uncharacterised gamma-7 having a similar conformation to gamma-5, with different functional properties not consistent with Bergmann glia AMPARs.
OpenNo structureIntrinsic dynamics of TARP gamma-7, set 2
James Krieger, Nayanika Sengupta, Alexander M. Scrutton, et al.
TARPs (transmembrane AMPA receptor regulatory proteins) are auxiliary subunits of AMPA-type glutamate receptors (AMPARs) that modulate receptor trafficking, gating, and pharmacology. Different TARPs bestow distinct functional properties on AMPARs, influencing synaptic transmission and plasticity. As part of a study on the Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum, we determined cryo-EM structures of native AMPARs in complex with TARPs, including GluA1/A4 heteromers with two TARPs, corresponding to the main Bergmann glia AMPAR. To help characterise these receptor complexes, the intrinsic dynamics of TARPs gamma-7 and gamma-2 in POPC membrane bilayer in the absence of the AMPAR was investigated using all-atom molecular dynamics simulations. Our simulations support gamma-7 as the main Bergmann glia TARP as they exhibit a straightening of transmembrane helix 2 (TM2) in 7 simulations, in line with a dominant cryo-EM class. By contrast, the well-studied TARP gamma-2 maintains a pronounced kink in TM2 characteristic of Type I TARPs for 100 ns in 3 simulations. Thus, MD simulations indicate that a straight TM2 is a hallmark of Type II TARPs with the previously uncharacterised gamma-7 having a similar conformation to gamma-5, with different functional properties not consistent with Bergmann glia AMPARs. To further validate that the gamma-7 TM2 helix straightening was not due to a bad starting model, a second set of simulations was run with some seemingly suboptimal contacts improved in PyMOL.
OpenNo structureIntrinsic dynamics of TARP gamma-7, set 1
James Krieger, Nayanika Sengupta, Alexander M. Scrutton, et al.
TARPs (transmembrane AMPA receptor regulatory proteins) are auxiliary subunits of AMPA-type glutamate receptors (AMPARs) that modulate receptor trafficking, gating, and pharmacology. Different TARPs bestow distinct functional properties on AMPARs, influencing synaptic transmission and plasticity. As part of a study on the Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum, we determined cryo-EM structures of native AMPARs in complex with TARPs, including GluA1/A4 heteromers with two TARPs, corresponding to the main Bergmann glia AMPAR. To help characterise these receptor complexes, the intrinsic dynamics of TARPs gamma-7 and gamma-2 in POPC membrane bilayer in the absence of the AMPAR was investigated using all-atom molecular dynamics simulations. Our simulations support gamma-7 as the main Bergmann glia TARP as they exhibit a straightening of transmembrane helix 2 (TM2) in 7 simulations, in line with a dominant cryo-EM class. By contrast, the well-studied TARP gamma-2 maintains a pronounced kink in TM2 characteristic of Type I TARPs for 100 ns in 3 simulations. Thus, MD simulations indicate that a straight TM2 is a hallmark of Type II TARPs with the previously uncharacterised gamma-7 having a similar conformation to gamma-5, with different functional properties not consistent with Bergmann glia AMPARs. To further validate that the gamma-7 TM2 helix straightening was not due to a bad starting model, a second set of simulations was run with some seemingly suboptimal contacts improved in PyMOL.
OpenNo structureDynaRepo 7ZR7
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns
OpenPDB 7ZR7Published 1 Oct 2025This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-RTP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
OpenPDB 6M71CC BY 4.0Published 21 Jan 2021Theoretical model generated using Modeller from the PDB 6vw1
OpenPDB 6VW1CC BY 4.0Published 16 Apr 2020Theoretical model generated using Modeller from the PDB 6vw1
OpenPDB 6VW1CC BY 4.0Published 21 Apr 2020Theoretical model generated using Modeller from the PDB 6vw1
OpenPDB 6VW1CC BY 4.0Published 20 Apr 2020