Lipid Membrane and Associated Protein Coordinates
Please cite our associated papers if these are used
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Model Cellular Membranes or Membrane-Associated Proteins
- Asymmetric Plasma Membrane models of the Stereocilia (Submitted): PDB/PSF
- Osh4 Dual Membrane Binding Model (BBA-Biomemb. 1866: 184365):PDB/PSF
- Age-based and Cataract Ocular Lens Membrane Models (BBA-Biomemb. 1864: 184025): (PDB/PSF) and (Par/Top)
- E. coli Inner Asymmetric Membrane models (JPCB. 126: p184 2022): (PDB/CRD/PSF with A/B/C cell in Header
- Arabidopsis thalina Asymmetric Membrane Models (JPCB. 125: p11418 2021): (PDB/CRD/PSF with A/B/C cell in Header and Par/Top)
- Stratum Corneum Long Periodicity Phase Membrane Models (JACS. 141: p16930 2019): (PDB/CRD/PSF with A/B/C cell in Header and Par/Top)
- CerEOS Pure Lipid Membranes (JPCB. 123: p2525 2019): (PDB/CRD/PSF with A/B/C cell in Header)
- P. Aeruginosa IM Models and Pure Lipid Membranes (Cer/FFA/CHOL) (JCP: 149: #215102 2018): (PDB/CRD/PSF with A/B/C cell in Header)
- More Simple Skin Models (Cer/FFA/CHOL) (JPCB: 122: p11996 2018): (PDB/CRD/PSF with A/B/C cell in Header)
- Simple Ocular Lens Models (Human and Bovine) (BBA Biomemb. 1860: p2134 2018): (PDB/CRD/PSF with A/B/C cell in Header)
- Simple Skin Models (CER/FFA/CHOL) (JPCB. 121: p2757 2018): (PDB/CRD/PSF with A/B/C cell in Header)
- Soy Plasma Membrane of Seedling (J. Chem. Phys. 2017): zipped files (HYPOCOTYL/ROOT/toppar)
- Yeast (Saccharomyces cerevisiae) organelle membranes (Biochemistry 2015): zipped files (ER1/ER2/TGN1/TGN2/PM1/PM2/Average/toppar)
- E. coli cytoplasmic membrane (CPL 2015): zipped files (Early log/Mid log/Stationary/Overnight)
- PSM and SSM bilayers (see BJ 2014): zipped files (PSM/SSM)
- Ester-modified lipid membranes (MGPC30 forms pores see Langmuir 2013): zipped file
- E. coli cytoplasmic membrane (6-lipid types at 303.15K from BBA 2012): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
- POPE/POPG (5.3:1 headgroup ratio) simple model of E. coli (303.15K from BBA 2012): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
- Chlamydia Membrane model for Elementary Body (9-lipid types at 303.15K from BBA 2011): PDB, CHARMM PSF, and X-Plor/NAMD PSF
- Chlamydia Membrane model for Reticular Body (9-lipid types at 303.15K from BBA 2011): PDB, CHARMM PSF, and X-Plor/NAMD PSF
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Single-Component Membranes (CHARMM36)
Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 or newer versions with vdwForceSwitching turned on.
- DHPC (ether lipid) Bilayer (333.15K, NPT, 100ns, 80 lipids): PDB/PSF/CRD
- DPHPC (branched lipid) Bilayer (303.15K, NPT, 50ns): PDB/PSF/CRD
- DPPC Bilayer (323.15K, NPT, 40ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
- DMPC Bilayer (303.00K, NPT, 40ns, 72 lipids): PDB and CHARMM PSF
- DOPC Bilayer (303.00K, NPT, 35ns, 72 lipids): PDB
- POPC Bilayer (303.00K, NPT, 35ns, 72 lipids): PDB and CHARMM PSF
- POPE Bilayer (310.15K, NPT, 40ns, 80 lipids): PDB,
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Single-Component Membranes (CHARMM27r)
Note: Use at your own risk as this is no longer the standard lipid FF in CHARMM (outdated).
- DPPC Bilayer (323.15K, A=64 Â/lipid, 50ns, 72 lipids): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
- DPPC Bilayer (323.15K, A=64 Â/lipid, 50ns, 288 lipids): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
- DMPC Bilayer (303.15K, A=60.7 Â/lipid, 50ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
- POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
- DPPC Monolayer (323.15K, A=64 Â/lipid, 25ns, 80 lipids): PDB, CHARMM PSF, and CHARMM CRD