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Citing the Resources
VIEW ALL ARTICLES IN PUBMED >>
Molecular Modeling Database (MMDB)
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...
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...
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]
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]
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: 10.1186/1472-6807-7-23. [PubMed PMID: 17425794]
[Full Text at BioMed Central]
more articles about VAST...
Additional Journal Articles
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]
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]
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]
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]
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]
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]
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]
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]
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]
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.2011.12.026. [PubMed PMID: 22198293]
[Full Text at Elsevier]
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]
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.2011.09.021. [PubMed PMID: 22153503]
[Full Text at Elsevier]
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]
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]
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]
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]
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]
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.2010.03.059. [PubMed PMID: 20381499]
[Full Text at Elsevier]
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.2009.10.052. [PubMed PMID: 19879880]
[Full Text at Elsevier]
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]
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]
Chakrabarti S, Panchenko AR.
Ensemble approach to predict specificity determinants: benchmarking and validation.
BMC Bioinformatics
2009
Jul 2; 10: 207. doi: 10.1186/1471-2105-10-207. [PubMed PMID: 19573245]
[Full Text at BioMed Central]
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]
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]
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.2009.04.096. [PubMed PMID: 19394310]
[Full Text at Elsevier]
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.2008.12.3904 [PubMed PMID: 19289044]
[Full Text at Elsevier]
[Erratum in: Biophys J. 2009 Jun 3;96(11):4753. doi: 10.1016/j.bpj.2009.05.002]
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]
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.2008.09.078. [PubMed PMID: 18930732]
[Full Text at Elsevier]
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]
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]
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: 10.1186/1471-2105-11-3]
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]
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]
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]
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]
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]
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]
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]
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]
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
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
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