Citations and acknowledgements

Use this page when preparing a manuscript, figure caption, data release, or software acknowledgement. Cite the three core entries for every VMDHole analysis. Then add only the entries for methods or quantities you report.

Cite for every VMDHole analysis

1. Ahangar, A. A. VMDHole (version used) [computer software]. https://github.com/aminkvh/VMDHole
2. Humphrey, W., Dalke, A. & Schulten, K. "VMD: Visual Molecular Dynamics." J. Mol. Graph. 14, 33-38 (1996). doi:10.1016/0263-7855(96)00018-5
3. Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A. & Sansom, M.S.P. "HOLE: A Program for the Analysis of the Pore Dimensions of Ion Channel Structural Models." J. Mol. Graph. 14, 354-360 (1996). doi:10.1016/S0263-7855(97)00009-X

Use the VMDHole version shown in Help → Guide & Citations…. If a versioned release DOI is available, use it in place of the repository URL.

Add citations for the analyses used

Pore geometry and conductance

• Connolly surface: Connolly, M.L. "Analytical Molecular Surface Calculation." J. Appl. Crystallogr. 16, 548-558 (1983). doi:10.1107/S0021889883010985
• Ellipse fit, ellipse volume, or ellipse conductance: Seiferth, D. & Biggin, P.C. "Exploring the Influence of Pore Shape on Conductance and Permeation." Biophys. J. 123, 3107-3119 (2024). doi:10.1016/j.bpj.2024.07.010
• Geometric conductance estimate: Smart, O.S., Breed, J., Smith, G.R. & Sansom, M.S.P. "A Novel Method for Structure-Based Prediction of Ion Channel Conductance Properties." Biophys. J. 72, 1109-1126 (1997). doi:10.1016/S0006-3495(97)78760-5
• Access resistance correction: Hall, J.E. "Access Resistance of a Small Circular Pore." J. Gen. Physiol. 66, 531-532 (1975). doi:10.1085/jgp.66.4.531
• Passability using hydrated or bare ion radii: Nightingale, E.R. "Phenomenological Theory of Ion Solvation. Effective Radii of Hydrated Ions." J. Phys. Chem. 63, 1381-1387 (1959). doi:10.1021/j150579a011; Pauling, L. The Nature of the Chemical Bond, 3rd ed. (1960).

Hydration and pore-wall annotations

• Hydration, water-density free energy, CHAP mode, or hydrophobic gating: Klesse, G., Rao, S., Sansom, M.S.P. & Tucker, S.J. "CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores." J. Mol. Biol. 431, 3353-3365 (2019). doi:10.1016/j.jmb.2019.06.003
• VMDHole pore-lining or pore-facing assignments: cite VMDHole. These surface-distance and orientation assignments are not PoreWalker classifications. Cite PoreWalker only when making a direct comparison: Pellegrini-Calace, M., Maiwald, T. & Thornton, J.M. "PoreWalker." PLoS Comput. Biol. 5, e1000440 (2009). doi:10.1371/journal.pcbi.1000440
• Automatic hydration KDE bandwidth: Silverman, B.W. Density Estimation for Statistics and Data Analysis (1986).
• Dry-bin lower bounds based on the rule of three: Hanley, J.A. & Lippman-Hand, A. "If Nothing Goes Wrong, Is Everything All Right?" JAMA 249, 1743-1745 (1983).

Tunnel analysis

• Tunnel mode: Sehnal, D., Svobodová Vařeková, R., Berka, K., Pravda, L., Navrátilová, V., Banáš, P., Ionescu, C.-M., Otyepka, M. & Koča, J. "MOLE 2.0: Advanced Approach for Analysis of Biomacromolecular Channels." J. Cheminform. 5, 39 (2013). doi:10.1186/1758-2946-5-39
• Tunnel clustering: Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J. & Damborsky, J. "CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures." PLoS Comput. Biol. 8, e1002708 (2012). doi:10.1371/journal.pcbi.1002708

Physicochemical maps

Cite a scale when its values are reported or used to support an interpretation.

Scale	Reference
Kyte-Doolittle	Kyte, J. & Doolittle, R.F. "A Simple Method for Displaying the Hydropathic Character of a Protein." J. Mol. Biol. 157, 105-132 (1982). doi:10.1016/0022-2836(82)90515-0
Wimley-White	Wimley, W.C. & White, S.H. "Experimentally Determined Hydrophobicity Scale for Proteins at Membrane Interfaces." Nat. Struct. Biol. 3, 842-848 (1996). doi:10.1038/nsb1096-842
Kapcha-Rossky	Kapcha, L.H. & Rossky, P.J. "A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure." J. Mol. Biol. 426, 484-498 (2014). doi:10.1016/j.jmb.2013.09.039
Grantham polarity	Grantham, R. "Amino Acid Difference Formula to Help Explain Protein Evolution." Science 185, 862-864 (1974). doi:10.1126/science.185.4154.862
Fauchere-Pliska lipophilicity	Fauchère, J.L. & Pliska, V. "Hydrophobic Parameters Pi of Amino-Acid Side Chains." Eur. J. Med. Chem. 18, 369-375 (1983).
Formal charge	Fersht, A.R. Structure and Mechanism in Protein Science (1999).

MOLE-derived tunnel properties, including hydropathy, hydrophobicity, polarity, charge, ionizable residues, LogP, LogD, LogS, and mutability, are covered by the MOLE 2.0 citation above.

Ion movement and trajectory alignment

• Voltage-driven computational electrophysiology trajectories: Kutzner, C., Grubmüller, H., de Groot, B.L. & Zachariae, U. "Computational Electrophysiology." Biophys. J. 101, 809-817 (2011). doi:10.1016/j.bpj.2011.06.010
• Align trajectory: acknowledge the VMD RMSD Trajectory Tool and Giorgino, T. "Computing 1-D Atomic Densities in Macromolecular Simulations." Comput. Phys. Commun. 185, 1109-1114 (2014). doi:10.1016/j.cpc.2013.11.019

Acknowledgements

The screen-space hydrophobicity scale bar adapts techniques from VMD's colorscalebar.tcl, by Wuwei Liang, Dan Wright, John Stone, and Axel Kohlmeyer.