3D Macromolecular Structures Publications

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Citing the Resources

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208. [PubMed PMID: 24319143] [Full Text at Oxford Academic]
more articles about MMDB... Click here to read

Cn3D

Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun; 25(6): 300-2. [PubMed PMID: 10838572] [Full Text at Elsevier]
more articles about Cn3D...

iCn3D

Jiyao Wang, Philippe Youkharibache, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Shennan Lu, Thomas Madej, Gabriele H Marchler, Tiejun Cheng, Li Chuin Chong, Sarah Zhao, Kevin Yang, Jack Lin, Zhiyu Cheng, Rachel Dunn, Sridhar Acharya Malkaram, Chin-Hsien Tai, David Enoma , Ben Busby, Nicholas L Johnson, Francesco Tabaro, Guangfeng Song, Yuchen Ge. iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode. Front Mol Biosci. 2022 Jan 1;36(1):131-135. (Epub 2019 June 20.) doi: 10.1093/bioinformatics/btz502. [Epub ahead of print] [PubMed PMID: 35252351] [Full Text at Frontiers in Molecular Biosciences]
more information about iCn3D... Click here to read

Vector Alignment Search Tool (VAST)

Citing VAST+:
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208. [PubMed PMID: 24319143] [Full Text at Oxford Academic] - and -
Madej T, Marchler-Bauer A, Lanczycki C, Zhang D, Bryant SH. Biological Assembly Comparison with VAST. Methods Mol Biol. 2020;2112:175-186. doi: 10.1007/978-1-0716-0270-6_13. [PubMed PMID: 32006286] [Full Text at Springer] Click here to read

Citing Original VAST: Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol. 1996 Jun; 6(3): 377-85. [PubMed PMID: 8804824] [Full Text at Elsevier]

Citing similarity scores: Panchenko AR, Madej T. Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins 2004 Nov 15; 57(3): 539-47. doi: 10.1002/prot.20237. [PubMed PMID: 15382231] [Full Text at Wiley Online Library] Click here to read

Citing homologous cores and loops: Madej T, Panchenko AR, Chen J, Bryant SH. Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins. BMC Struct Biol. 2007 Apr 10; 7(1): 23. doi: 10.1186/1472-6807年7月23日. [PubMed PMID: 17425794] [Full Text at BioMed Central]

more articles about VAST... Click here to read

Additional Journal Articles
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Sayers EW, Beck J, Bolton EE, Brister JR, Chan J, Comeau DC, Connor R, DiCuccio M, Farrell CM, Feldgarden M, Fine AM, Funk K, Hatcher E, Hoeppner M, Kane M, Kannan S, Katz KS, Kelly C, Klimke W, Kim S, Kimchi A, Landrum M, Lathrop S, Lu Z, Malheiro A, Marchler-Bauer A, Murphy TD, Phan L, Prasad AB, Pujar S, Sawyer A, Schmieder E, Schneider VA, Schoch CL, Sharma S, Thibaud-Nissen F, Trawick BW, Venkatapathi T, Wang J, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2023 Nov 22. doi: 10.1093/nar/gkad1044. [PubMed PMID: 37994677] [Full Text at Oxford Academic]

Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Farrell CM, Feldgarden M, Fine AM, Funk K, Hatcher E, Kannan S, Kelly C, Kim S, Klimke W, Landrum MJ, Lathrop S, Lu Z, Madden TL, Malheiro A, Marchler-Bauer A, Murphy TD, Phan L, Pujar S, Rangwala SH, Schneider VA, Tse T, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D29-D38. doi: 10.1093/nar/gkac1032. [PubMed PMID: 36370100] [Full Text at Oxford Academic] Click here to read

Niesen MJM, Murugadoss K, Lenehan PJ, Marchler-Bauer A, Wang J, Connor R, Brister JR, Venkatakrishnan AJ, Soundararajan V. Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure. PNAS Nexus. 2022 Jul 4;1(3):pgac105. doi: 10.1093/pnasnexus/pgac105. eCollection 2022 Jul.[PubMed PMID: 35899067] [Full Text at PubMed Central] Click here to read

Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2021 Dec 1. doi: 10.1093/nar/gkab1112. [PubMed PMID: 34850941] [Full Text at Oxford Academic] Click here to read

Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures. Bioinformatics. 2020 Jan 1;36(1):131-135. (Epub 2019 June 20.) doi: 10.1093/bioinformatics/btz502. [Epub ahead of print] [PubMed PMID: 31218344] [Full Text at Oxford Academic] Click here to read

Youkharibache P, Cachau R, Madej T, Wang J. Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. bioRxiv. 2020 Jul 2. doi: 10.1101/2020.07.01.182964. [PubMed PMID: 32637961] [Full Text at Cold Spring Harbor Laboratory] Click here to read

Roy Choudhury A, Cheng T, Phan L, Bryant SH, Wang Y. Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites. Bioinformatics 2017 2017 Jun 1;33(11):1621-1629. (Epub 2017 Jan 31.) doi: 10.1093/bioinformatics/btx031. [PubMed PMID: 28158543] [Full Text at Oxford Academic] Click here to read

Pan Y, Cheng T, Wang Y, Bryant SH. Pathway Analysis for Drug Repositioning Based on Public Database Mining. J Chem Inf Model. 2014 Feb 24;54(2):407-18.(Epub 2014 Feb 5.) doi: 10.1021/ci4005354 [PubMed PMID: 24460210] [Full Text at ACS Publications] Click here to read

Tyagi M, Thangudu RR, Zhang D, Bryant SH, Madej T, Panchenko AR. Homology inference of protein-protein interactions via conserved binding sites. PLoS One 2012 7(1):e28896. Epub 2012 Jan 31. doi: 10.1371/journal.pone.0028896. [PubMed PMID: 22303436] [Full Text at PLoS] Click here to read

Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR. Large-scale mapping of human protein interactome using structural complexes. EMBO Rep. 2012 Mar 1;13(3):266-71. (Epub 2012 Jan 20) doi: 10.1038/embor.2011.261. [PubMed PMID: 22261719] [Full Text at EMBO Press] Click here to read

Thangudu RR, Bryant SH, Panchenko AR, Madej T. Modulating Protein-Protein Interactions with Small Molecules: The Importance of Binding Hotspots. J Mol Biol 2012 Jan 13;415(2):443-53. (Epub 2011 Dec 16) doi: 10.1016/j.jmb.2011年12月02日6. [PubMed PMID: 22198293] [Full Text at Elsevier] Click here to read

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D461-4. doi: 10.1093/nar/gkr1162. Epub 2011 Dec 1. doi: 10.1093/nar/gkr1162. [PubMed PMID: 22135289] [Full Text at Oxford Academic] Click here to read

Nishi H, Hashimoto K, Panchenko AR. Phosphorylation in protein-protein binding: effect on stability and function. Structure 2011 Dec 7;19(12):1807-1815. doi: 10.1016/j.str.2011年09月02日1. [PubMed PMID: 22153503] [Full Text at Elsevier] Click here to read

Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 2012 Jan; 40(1):D834-40. Epub 2011 Nov 18. doi: 10.1093/nar/gkr997. [PubMed PMID: 22102591] [Full Text at Oxford Academic] Click here to read

Hashimoto K, Nishi H, Bryant S, Panchenko AR. Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. Phys Biol. 2011 Jun; 8(3):035007. (Epub 2011 May 13) doi: 10.1088/1478-3975/8/3/035007. [PubMed PMID: 21572178] [Full Text at IOP Publishing] Click here to read

Hashimoto K, Panchenko AR. Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc Natl Acad Sci U S A 2010 Nov 23; 107(47):20352-7. (Epub 2010 Nov 3) doi: 10.1073/pnas.1012999107. [PubMed PMID: 21048085] [Full Text at PNAS] Click here to read

Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T. Knowledge-based annotation of small molecule binding sites in proteins. Bioinformatics 2010 Jul 1; 11: 365. doi: 10.1186/1471-2105-11-365. [PubMed PMID: 20594344] Click here to read

Fong JH, Panchenko AR. Intrinsic disorder and protein multibinding in domain, terminal, and linker regions. Mol Biosyst. 2010 Oct 1; 6(10): 1821-8. (Epub 2010 Jun 11) doi: 10.1039/c005144f. [PubMed PMID: 20544079] Click here to read

Hashimoto K, Madej T, Bryant SH, Panchenko AR. Functional states of homooligomers: insights from the evolution of glycosyltransferases. J Mol Biol. 2010 May 28;399(1):196-206. (Epub 2010 Apr 8) doi: 10.1016/j.jmb.2010年03月05日9. [PubMed PMID: 20381499] [Full Text at Elsevier] Click here to read

Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR. Evolution of protein binding modes in homooligomers. J Mol Biol. 2010 Jan 29; 395(4):860-70. Epub 2009 Oct 30. doi: 10.1016/j.jmb.2009年10月05日2. [PubMed PMID: 19879880] [Full Text at Elsevier] Click here to read

Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 2010 Jan; 38(Database issue): D518-24. doi: 10.1093/nar/gkp842 [PubMed PMID: 19843613] Click here to read

Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR. Exploring functional roles of multibinding protein interfaces. Protein Sci. 2009 Aug; 18(8):1674-83. doi: 10.1002/pro.181. [PubMed PMID: 19591200] [Full Text at Wiley Online Library] Click here to read

Chakrabarti S, Panchenko AR. Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 2009 Jul 2; 10: 207. doi: 10.1186/1471-2105年10月20日7. [PubMed PMID: 19573245] [Full Text at BioMed Central] Click here to read

Fong JH, Marchler-Bauer A. CORAL: aligning conserved core regions across domain families. Bioinformatics 2009 Aug 1; 25(15): 1862-8. Epub 2009 May 26. doi: 10.1093/bioinformatics/btp334. [PubMed PMID: 19470584] [Full Text at Oxford Academic] Click here to read

Thompson KE, Wang Y, Madej T, Bryant SH. Improving protein structure similarity searches using domain boundaries based on conserved sequence information. BMC Struct Biol. 2009 May 19; 9: 33. doi: 10.1186/1472-6807-9-33. [PubMed PMID: 19454035] [Full Text at BioMed Central] Click here to read

Tang K, Pugalenthi G, Suganthan PN, Lanczycki CJ, Chakrabarti S. Prediction of functionally important sites from protein sequences using sparse kernel least squares classifiers. Biochem Biophys Res Commun. 2009 Jun 26; 384(2): 155-9. Epub 2009 Apr 24. doi: 10.1016/j.bbrc.2009年04月09日6. [PubMed PMID: 19394310] [Full Text at Elsevier] Click here to read

Teng S, Madej T, Panchenko A, Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J. 2009 Mar 18; 96(6):2178-88. doi: 10.1016/j.bpj.2008123904 [PubMed PMID: 19289044] [Full Text at Elsevier] [Erratum in: Biophys J. 2009 Jun 3;96(11):4753. doi: 10.1016/j.bpj.200905002] Click here to read

Fong JH, Shoemaker BA, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, Panchenko AR. Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. PLoS Comput Biol. 2009 Mar; 5(3):e1000316. Epub 2009 Mar 13. doi: 10.1371/journal.pcbi.1000316. [PubMed PMID: 19282967] [Full Text at PLoS] Click here to read

Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM. Correlated evolution of interacting proteins: looking behind the mirrortree. J Mol Biol. 2009 Jan 9; 385(1):91-8. Epub 2008 Oct 9. doi: 10.1016/j.jmb.2008年09月07日8. [PubMed PMID: 18930732] [Full Text at Elsevier] Click here to read

Chakrabarti S, Panchenko AR. Coevolution in defining the functional specificity. Proteins 2009 Apr; 75(1):231-40. doi: 10.1002/prot.22239. [PubMed PMID: 18831050] [Full Text at Wiley Online Library] Click here to read

Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, Zhang N, Bryant SH. MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res. 2007 Jan; 35(Database issue): D298-300. doi: 10.1093/nar/gkl952 [PubMed PMID: 17135201] [Full Text at Oxford Academic] Click here to read

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH. State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006 Nov 14; 7:499. doi: 10.1186/1471-2105-7-499. [PubMed PMID: 17105653] [Full Text at BioMed Central] [Erratum in: BMC Bioinformatics. 2010;11:3. doi: 10.1186/1471-2105年11月3日] Click here to read

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH. Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res. 2006 May 17; 34(9):2598-606. doi: 10.1093/nar/gkl274. [PubMed PMID: 16707662] [Full Text at Oxford Academic] Click here to read

Kann MG, Thiessen PA, Panchenko AR, Schäffer AA, Altschul SF, Bryant SH. A structure-based method for protein sequence alignment. Bioinformatics 2005 Apr 15; 21(8):1451-6. Epub 2004 Dec 21. doi: 10.1093/bioinformatics/bti233. [PubMed PMID: 15613392] [Full Text at Oxford Academic]

Panchenko AR, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci. 2004 Apr; 13(4):884-92. Epub 2004 Mar 9. doi: 10.1110/ps.03465504. [PubMed PMID: 15010543] [Full Text at Wiley Online Library] Click here to read

Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2003 Jan; 31(1): 474-7. [PubMed PMID: 12520055] [Full Text at Oxford Academic] Click here to read

Panchenko AR, Bryant SH. A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 2002 Feb; 11(2):361-70. doi: 10.1110/ps.19902. [PubMed PMID: 11790846] [Full Text at Wiley Online Library] Click here to read

Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2002 Jan 1;30(1):249-52. [PubMed PMID: 11752307] [Full Text at Oxford Academic] Click here to read

Wang Y, Bryant S, Tatusov R, Tatusova T. Links from genome proteins to known 3-D structures. Genome Res. 2000 Oct; 10(10):1643-7. [PubMed PMID: 11042161] [Full Text at CSH Press] Click here to read

Wang Y, Addess KJ, Geer L, Madej T, Marchler-Bauer A, Zimmerman D, Bryant SH. MMDB: 3D structure data in Entrez. Nucleic Acids Res. 2000 Jan 1;28(1):243-5. [PubMed PMID: 10592236] [Full Text at Oxford Academic] Click here to read

Matsuo Y, Bryant SH. Identification of homologous core structures. Proteins 1999 Apr 1;35(1):70-9. [PubMed PMID: 10090287]

Marchler-Bauer A, Addess KJ, Chappey C, Geer L, Madej T, Matsuo Y, Wang Y, Bryant SH. MMDB: Entrez's 3D structure database. Nucleic Acids Res. 1999 Jan 1;27(1):240-3. [PubMed PMID: 9847190] [Full Text at Oxford Academic] Click here to read

Hogue CW. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem Sci. 1997 Aug; 22(8):314-6. [PubMed PMID: 9270306] [Full Text at Elsevier]

Bryant SH and Hogue CW. Structural neighbors and structural alignments: The science behind Entrez/3D. Presented at the IUCr Macromolecular Crystallography Computing School, August 1996.

Hogue CW, Ohkawa H, Bryant SH. A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci. 1996 Jun;21(6):226-9. [PubMed PMID: 8744358] [Full Text at Elsevier]

Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995 Nov; 23(3):356-69. doi: 10.1002/prot.340230309. [PubMed PMID: 8710828] [Full Text at Wiley Online Library]

Ohkawa H, Ostell J, Bryant S. MMDB: an ASN.1 specification for macromolecular structure. Proc Int Conf Intell Syst Mol Biol. 1995;3:259-67. [PubMed PMID: 7584445]

Bryant SH. PKB: a program system and data base for analysis of protein structure. Proteins 1989; 5(3):233-47. doi: 10.1002/prot.340050307. [PubMed PMID: 2780541] [Full Text at Wiley Online Library]

Book Chapters back to top

Sayers E. NCBI Protein Resources. IN The NCBI Handbook, 2nd edition [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2013 Nov. 12, 2013 [revised 2013 Nov. 21]. [cited 2017 Feb 02]. Available from /books/NBK169830/ in Entrez Books (/books).

Sayers E, Bryant SH. Macromolecular Structure Databases. Chapter 3 IN The NCBI Handbook [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2002 Oct. 9 [revised 2003 Aug. 13]. [cited 2009 Feb 04]. Available from /books/NBK21095/ in Entrez Books (/books).

Revised 1 December 2023