FirstGlance in Jmol Literature Citations

From Proteopedia

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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

• FirstGlance in Jmol
• Unique Capabilities of FirstGlance in Jmol
• FirstGlance YouTube Channel
• FirstGlance/Index, a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
• Start FirstGlance in Jmol

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

• O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.

• 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

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

• Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.

"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

• 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.)

• Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).

• 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

• Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.

Figure 1A to be inserted here pending permission.

• 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.

• 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

Fig. 3C to go here pending permission.

• 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.

• Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.

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

• Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.

• Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.

• Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.

• 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

• 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

• 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

2016-2020

Education & Communication

• Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.

BioMedical Research

• 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

• 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."

• Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.

• 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

• Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078..

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."