VAST: Vector Alignment Search Tool
Citing 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]
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  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]  
  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. [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. [PubMed PMID: 17425794] [Full Text at BioMed Central] Click here to read
Additional Journal Articles
  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. [PubMed PMID: 19454035] [Full Text at BioMed Central] 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. [PubMed PMID: 11790846] [Full Text at Wiley Online Library] Click here to read
  Matsuo Y, Bryant SH. Identification of homologous core structures. Proteins 1999 Apr 1;35(1):70-9. [PubMed PMID: 10090287]  
  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]  
    (See all publications about NCBI's 3D Macromolecular Structures Resources, including those listed here plus articles by the NCBI Structure group describing the results of computational biology research on the Molecular Modeling Database, such as 3D structure comparisons, biomolecular interactions, and more.)  
Revised 09 February 2021