FirstGlance in Jmol Literature Citations

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Revision as of 20:52, 1 May 2025

The following publications in the scientific literature cite use of FirstGlance in Jmol. This list excludes publications co-authored by User:Eric Martz, the author of FirstGlance in Jmol. (Those are listed at Google Scholar: Eric Martz.) The citations below were found by searching full text using Google Scholar, and all were verified to cite FirstGlance in Jmol.

FirstGlance in Jmol offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average 265 times/day. For more, see

__NOTOC_

Contents

2021-2025

Education & Communication

  • Mokos D, Daniel B. Interactive 3D Objects Enhance Scientific Communication of Structural Data. Chembiochem. 2025 Mar 15;26(6):e202500036. PMID:39976303 doi:10.1002/cbic.202500036
  • Rose A, Sehnal D, Goodsell DS, Autin L. Mesoscale explorer: Visual exploration of large-scale molecular models. Protein Sci. 2024 Oct;33(10):e5177. PMID:39291955 doi:10.1002/pro.5177
  • Procko K, Bakheet S, Beckham JT, Franzen MA, Jakubowski H, Novak WRP. Modeling an Enzyme Active Site using Molecular Visualization Freeware. J Vis Exp. 2021 Dec 25;(178). PMID:35001912 doi:10.3791/63170

BioMedical Research

2025

Figure 5 from García, 2025. Molecular rendering of 4x36 by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).

  • García E. Structure, Function, and Regulation of LytA: The N-Acetylmuramoyl-l-alanine Amidase Driving the "Suicidal Tendencies" of Streptococcus pneumoniae-A Review. Microorganisms. 2025 Apr 5;13(4):827. PMID:40284663 doi:10.3390/microorganisms13040827
"AlphaFold 2 modeling of HIR2 and analysis of the distribution of polar amino acids by FirstGlance revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."
  • Yao X, Lu WH, Qiao WT, Zhang YQ, Zhang BY, Li HX, Li JL. The highly pathogenic strain of porcine deltacoronavirus disrupts the intestinal barrier and causes diarrhea in newborn piglets. Virulence. 2025 Dec;16(1):2446742. PMID:39758030 doi:10.1080/21505594.2024.2446742

2024

Fig. 1, 1ol5, from Martinez et al., 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez et al.. Reproduced in accord with the Creative Commons Attribution Deed[1].

  • Nabi T, Riyed TH, Ornob A. Deep learning based predictive modeling to screen natural compounds against TNF-alpha for the potential management of rheumatoid arthritis: Virtual screening to comprehensive in silico investigation. PLoS One. 2024 Dec 5;19(12):e0303954. PMID:39636801 doi:10.1371/journal.pone.0303954
FirstGlance in Jmol was used to visualize and tabulate missing residues in 2az5. (See Missing residues and incomplete sidechains.)
  • Cerella C, Gajulapalli SR, Lorant A, Gerard D, Muller F, Lee Y, Kim KR, Han BW, Christov C, Récher C, Sarry JE, Dicato M, Diederich M. ATP1A1/BCL2L1 predicts the response of myelomonocytic and monocytic acute myeloid leukemia to cardiac glycosides. Leukemia. 2024 Jan;38(1):67-81. PMID:37904054 doi:10.1038/s41375-023-02076-8
  • Rajam SM, Varghese PC, Shirude MB, Syed KM, Devarajan A, Natarajan K, Dutta D. Kinase activity of histone chaperone APLF maintains steady state of centrosomes in mouse embryonic stem cells. Eur J Cell Biol. 2024 Sep;103(3):151439. PMID:38968704 doi:10.1016/j.ejcb.2024.151439
FirstGlance was used to visualize models predicted by AlphaFold2, colored by reliablity scores.

Fig. 3C, and AlphaFold2 prediction, from Gajda et al., 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution Deed[1].

  • Gajda Ł, Daszkowska-Golec A, Świątek P. Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis. Int J Mol Sci. 2024 Apr 25;25(9):4685. PMID:38731903 doi:10.3390/ijms25094685
  • Li R, Song X, Shan S, Hussain Dhiloo K, Wang S, Yin Z, Lu Z, Khashaveh A, Zhang Y. Female-Biased Odorant Receptor MmedOR48 in the Parasitoid Microplitis mediator Broadly Tunes to Plant Volatiles. J Agric Food Chem. 2024 Aug 7;72(31):17617-17625. PMID:39052973 doi:10.1021/acs.jafc.4c02737
Transmembrane secondary structure segments were evaluated using FirstGlance prior to docking analysis.
FirstGlance was used to locate mutations in the 3D structure.

2023

  • García E. Two putative glutamate decarboxylases of Streptococcus pneumoniae as possible antigens for the production of anti-GAD65 antibodies leading to type 1 diabetes mellitus. Int Microbiol. 2023 Aug;26(3):675-690. PMID:37154976 doi:10.1007/s10123-023-00364-y
  • Garduño-Sánchez MAA, De Jesus-Bonilla V, Perea S, Miranda-Gamboa R, Herrera-García A, De la Maza Benignos M, Ornelas-García CP. Mitochondrial phylogeography and molecular evolution of the rhodopsin visual pigment in troglobitic populations of Astyanax mexicanus (De Filippi, 1853). Zool Res. 2023 Jul 18;44(4):761-775. PMID:37464933 doi:10.24272/j.issn.2095-8137.2022.437
  • Yao X, Qiao WT, Zhang YQ, Lu WH, Wang ZW, Li HX, Li JL. A new PEDV strain CH/HLJJS/2022 can challenge current detection methods and vaccines. Virol J. 2023 Jan 20;20(1):13. PMID:36670408 doi:10.1186/s12985-023-01961-z

2022

Graphical Abstract from Puccio et al., 2022. Molecular rendering by FirstGlance in Jmol. Red and Blue planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed[2].

  • Puccio T, Kunka KS, An SS, Kitten T. Contribution of a ZIP-family protein to manganese uptake and infective endocarditis virulence in Streptococcus sanguinis. Mol Microbiol. 2022 Feb;117(2):353-374. PMID:34855265 doi:10.1111/mmi.14853
"Positions within a cellular membrane were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."
  • Budania S, Dubey A, Singh A. Trypanosoma evansi RoTat 1.2 variant surface antigen mimotopes selected by panning of the random peptide phage-display library against monoclonal antibodies. J Mol Recognit. 2022 Nov;35(11):e2984. PMID:35869579 doi:10.1002/jmr.2984
  • Peter J, Huleux M, Spaniol B, Sommer F, Neunzig J, Schroda M, Li-Beisson Y, Philippar K. Fatty acid export (FAX) proteins contribute to oil production in the green microalga Chlamydomonas reinhardtii. Front Mol Biosci. 2022 Aug 30;9:939834. PMID:36120551 doi:10.3389/fmolb.2022.939834
  • Ting TY, Baharin A, Ramzi AB, Ng CL, Goh HH. Neprosin belongs to a new family of glutamic peptidase based on in silico evidence. Plant Physiol Biochem. 2022 Jul 15;183:23-35. PMID:35537348 doi:10.1016/j.plaphy.2022.04.027

Figure 5 from Camelo et al., 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed[3].

  • Quinn JE, Jeninga MD, Limm K, Pareek K, Meißgeier T, Bachmann A, Duffy MF, Petter M. The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression. Front Cell Dev Biol. 2022 Apr 12;10:816558. PMID:35493110 doi:10.3389/fcell.2022.816558
  • Khalilullah H, Agarwal DK, Ahsan MJ, Jadav SS, Mohammed HA, Khan MA, Mohammed SAA, Khan R. Synthesis and Anti-Cancer Activity of New Pyrazolinyl-Indole Derivatives: Pharmacophoric Interactions and Docking Studies for Identifying New EGFR Inhibitors. Int J Mol Sci. 2022 Jun 11;23(12):6548. PMID:35742992 doi:10.3390/ijms23126548
  • Al Kufi SGJH, Emmerson J, Rosenqvist H, Garcia CMM, Rios-Szwed DO, Wiese M. Absence of DEATH kinesin is fatal for Leishmania mexicana amastigotes. Sci Rep. 2022 Feb 28;12(1):3266. PMID:35228627 doi:10.1038/s41598-022-07412-z
  • Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Reyes-Leyva J, Santos-López G, Rivera-Benítez JF, Rosas-Murrieta NH. Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential. PLoS One. 2022 Feb 9;17(2):e0263582. PMID:35139120 doi:10.1371/journal.pone.0263582

2021

  • Rubin M, Ben-Tal N. Using ConSurf to Detect Functionally Important Regions in RNA. Curr Protoc. 2021 Oct;1(10):e270. PMID:34619810 doi:10.1002/cpz1.270
  • Loza-Muller L, Shitan N, Yamada Y, Vázquez-Flota F. AmABCB1, an alkaloid transporter from seeds of Argemone mexicana L (Papaveraceae). Planta. 2021 Nov 16;254(6):122. PMID:34786595 doi:10.1007/s00425-021-03780-4

2016-2020

Education & Communication

  • Lee NY, Tucker-Kellogg G. An accessible, open-source mobile application for macromolecular visualization using augmented reality. Biochem Mol Biol Educ. 2020 May;48(3):297-303. PMID:32077575 doi:10.1002/bmb.21335
Lee et al., 2020, said "... browser-based applications or interfaces (e.g., FirstGlance in Jmol) increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."

BioMedical Research

2020

Fig. 2d from Lin et al., 2020. Secondary structure percentages and molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International Deed[4].

  • Lin M, Jin Y, Chen X, Sui Y, Li Y, Li H, Ni X, Zhao N, Lu Y, Jiang M. Increased hydrophobicity of CRYGD p.(Ala159ProfsTer9): Suspected cause of congenital cataracts in a large Chinese family. Mol Genet Genomic Med. 2020 Oct;8(10):e1436. PMID:33460241 doi:10.1002/mgg3.1436
  • Ben Chorin A, Masrati G, Kessel A, Narunsky A, Sprinzak J, Lahav S, Ashkenazy H, Ben-Tal N. ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. Protein Sci. 2020 Jan;29(1):258-267. PMID:31702846 doi:10.1002/pro.3779
Ben Chorin et al., 2020, wrote "The conservation grades (colors) are mapped onto the three-dimensional structure of the query protein, which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."
  • Pollack JD, Gerard D, Makhatadze GI, Pearl DK. Evolutionary conservation and structural localizations suggest a physical trace of metabolism's progressive geochronological emergence. J Biomol Struct Dyn. 2020 Aug;38(12):3700-3719. PMID:31608807 doi:10.1080/07391102.2019.1679666

Portions of Fig. 2I,J from McGurk et al., 2020. The tankyrase-binding-domain of 4bs2 was identified (yellow halos) with the Find tool of FirstGlance in Jmol. FirstGlance also added the sequence labels. Reproduced in accord with the Creative Commons Attribution 4.0 International Deed[1].

  • McGurk L, Rifai OM, Bonini NM. TDP-43, a protein central to amyotrophic lateral sclerosis, is destabilized by tankyrase-1 and -2. J Cell Sci. 2020 Jun 23;133(12):jcs245811. PMID:32409565 doi:10.1242/jcs.245811
  • Hong Y, Lee J, Vu TH, Lee S, Lillehoj HS, Hong YH. Immunomodulatory effects of avian β-defensin 5 in chicken macrophage cell line. Res Vet Sci. 2020 Oct;132:81-87. PMID:32531564 doi:10.1016/j.rvsc.2020.06.002
Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... Files were kept if their Rfree grade was at least "average" at their resolution."
  • Mattila HK, Mäkinen M, Lundell T. Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. Biotechnol Biofuels. 2020 Feb 24;13:26. PMID:32123543 doi:10.1186/s13068-020-01677-0
Mattila et al. 2020 provided a downloadable PDB file with a link to view it by uploading to FirstGlance in Jmol.
  • Hong Y, Lee J, Vu TH, Lee S, Lillehoj HS, Hong YH. Chicken avian β-defensin 8 modulates immune response via the mitogen-activated protein kinase signaling pathways in a chicken macrophage cell line. Poult Sci. 2020 Sep;99(9):4174-4182. PMID:32867961 doi:10.1016/j.psj.2020.05.027

2019

  • Eozenou C, Bashamboo A, Bignon-Topalovic J, Merel T, Zwermann O, Lourenco D, Lottmann H, Lichtenauer U, Rojo S, Beuschlein F, McElreavey K, Brauner R. The TALE homeodomain of PBX1 is involved in human primary testis-determination. Hum Mutat. 2019 Aug;40(8):1071-1076. PMID:31058389 doi:10.1002/humu.23780
  • Tuvi-Arad I, Alon G. Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. J Cheminform. 2019 Jun 6;11(1):39. PMID:31172379 doi:10.1186/s13321-019-0360-9

2017

  • Naasse Y, Bakhchane A, Charoute H, Jennane F, Bignon-Topalovic J, Malki A, Bashamboo A, Barakat A, Rouba H, McElreavey K. A Novel Homozygous Missense Mutation in the FU-CRD2 Domain of the R-spondin1 Gene Associated with Familial 46,XX DSD. Sex Dev. 2017;11(5-6):269-274. PMID:29262419 doi:10.1159/000485393

2011-2015

Education & Communication

  • Craig PA, Michel LV, Bateman RC. A survey of educational uses of molecular visualization freeware. Biochem Mol Biol Educ. 2013 May-Jun;41(3):193-205. PMID:23649886 doi:10.1002/bmb.20693
  • Barber NC, Stark LA. Engaging with molecular form to understand function. CBE Life Sci Educ. 2014 Spring;13(1):21-4. PMID:24591499 doi:10.1187/cbe.13-12-0247
Barber & Stark said "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."
  • Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. Biochem Mol Biol Educ. 2013 Sep-Oct;41(5):351-9. doi: 10.1002/bmb.20718. Epub, 2013 Sep 10. PMID:24019219 doi:http://dx.doi.org/10.1002/bmb.20718

2006-2010

Education & Communication

  • Berry C, Baker MD. Inside protein structures: Teaching in three dimensions. Biochem Mol Biol Educ. 2010 Nov;38(6):425-9. PMID:21567875 doi:10.1002/bmb.20434
... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....
  • McMahon B, Hanson RM. A toolkit for publishing enhanced figures. J Appl Crystallogr. 2008 Aug 1;41(Pt 4):811-814. Epub 2008 Jul 1. PMID:19461848 doi:10.1107/S0021889808015616
Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....
  • Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."

References

  1. ↑ 1.0 1.1 1.2 This work was published under the Creative Commons Attribution 4.0 International Deed.
  2. ↑ This work was published under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed.
  3. ↑ This work was published under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed.
  4. ↑ This work was published under the Creative Commons Attribution-NonCommercial 4.0 International Deed.

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