FirstGlance in Jmol Literature Citations

From Proteopedia

Revision as of 17:03, 29 April 2025

FirstGlance in Jmol offers 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. 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

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. These citations were found by searching full text using Google Scholar, and all were verified to cite 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

• 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

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

BioMedical Research

• 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

• 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).

• 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.

• 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

• 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

• 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

• 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

• 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

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."

• 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

• 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