MOLMOL: a program for display and analysis of macromolecular structures - PubMed (original) (raw)

MOLMOL: a program for display and analysis of macromolecular structures

R Koradi et al. J Mol Graph. 1996 Feb.

Abstract

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

PubMed Disclaimer

Similar articles

• Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.
  Billeter M, Qian YQ, Otting G, Müller M, Gehring W, Wüthrich K. Billeter M, et al. J Mol Biol. 1993 Dec 20;234(4):1084-93. doi: 10.1006/jmbi.1993.1661. J Mol Biol. 1993. PMID: 7903398
• Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain.
  Qian YQ, Otting G, Billeter M, Müller M, Gehring W, Wüthrich K. Qian YQ, et al. J Mol Biol. 1993 Dec 20;234(4):1070-83. doi: 10.1006/jmbi.1993.1660. J Mol Biol. 1993. PMID: 7903397
• The NMR solution structure of the non-classical homeodomain from the rat liver LFB1/HNF1 transcription factor.
  Schott O, Billeter M, Leiting B, Wider G, Wüthrich K. Schott O, et al. J Mol Biol. 1997 Apr 4;267(3):673-83. doi: 10.1006/jmbi.1997.0905. J Mol Biol. 1997. PMID: 9126845
• Hydration of biological macromolecules in solution: surface structure and molecular recognition.
  Wüthrich K. Wüthrich K. Cold Spring Harb Symp Quant Biol. 1993;58:149-57. doi: 10.1101/sqb.1993.058.01.019. Cold Spring Harb Symp Quant Biol. 1993. PMID: 7525144 Review. No abstract available.
• Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.
  Surles MC, Richardson JS, Richardson DC, Brooks FP Jr. Surles MC, et al. Protein Sci. 1994 Feb;3(2):198-210. doi: 10.1002/pro.5560030205. Protein Sci. 1994. PMID: 8003957 Free PMC article. Review.

Cited by

• Conopeptide ρ-TIA defines a new allosteric site on the extracellular surface of the α1B-adrenoceptor.
  Ragnarsson L, Wang CI, Andersson Å, Fajarningsih D, Monks T, Brust A, Rosengren KJ, Lewis RJ. Ragnarsson L, et al. J Biol Chem. 2013 Jan 18;288(3):1814-27. doi: 10.1074/jbc.M112.430785. Epub 2012 Nov 26. J Biol Chem. 2013. PMID: 23184947 Free PMC article.
• Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site.
  Fujiwara Y, Goda N, Tamashiro T, Narita H, Satomura K, Tenno T, Nakagawa A, Oda M, Suzuki M, Sakisaka T, Takai Y, Hiroaki H. Fujiwara Y, et al. Protein Sci. 2015 Mar;24(3):376-85. doi: 10.1002/pro.2628. Epub 2015 Jan 13. Protein Sci. 2015. PMID: 25534554 Free PMC article.
• Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human.
  Wang Y, Yesselman JD, Zhang Q, Kang M, Feigon J. Wang Y, et al. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5125-34. doi: 10.1073/pnas.1607411113. Epub 2016 Aug 16. Proc Natl Acad Sci U S A. 2016. PMID: 27531956 Free PMC article.
• The PCI domains are "winged" HEAT domains.
  Paul EE, Marintchev A. Paul EE, et al. PLoS One. 2022 Sep 12;17(9):e0268664. doi: 10.1371/journal.pone.0268664. eCollection 2022. PLoS One. 2022. PMID: 36094910 Free PMC article.
• Selectivity in post-translational biotin addition to five human carboxylases.
  Ingaramo M, Beckett D. Ingaramo M, et al. J Biol Chem. 2012 Jan 13;287(3):1813-22. doi: 10.1074/jbc.M111.275982. Epub 2011 Nov 28. J Biol Chem. 2012. PMID: 22123817 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Elsevier Science

• Other Literature Sources

  • The Lens - Patent Citations Database