메뉴 건너뛰기




Volumn 30, Issue 16, 2014, Pages 2288-2294

Improving B-cell epitope prediction and its application to global antibody-antigen docking

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN ANTIBODY COMPLEX; EPITOPE;

EID: 84906235282     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu190     Document Type: Article
Times cited : (140)

References (25)
  • 1
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman, H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 2
    • 84871743002 scopus 로고    scopus 로고
    • One target-two different binding modes: Structural insights into gevokizumab and canakinumab interactions to interleukin-1β (il-1β)
    • Blech, M. et al. (2012) One target-two different binding modes: structural insights into gevokizumab and canakinumab interactions to interleukin-1β (il-1β). J. Mol. Biol., 425, 94-111.
    • (2012) J. Mol. Biol , vol.425 , pp. 94-111
    • Blech, M.1
  • 3
    • 84870440262 scopus 로고    scopus 로고
    • Application of asymmetric statistical potentials to antibody- protein docking
    • Brenke, R. et al. (2012) Application of asymmetric statistical potentials to antibody- protein docking. Bioinformatics, 28, 2608-2614.
    • (2012) Bioinformatics , vol.28 , pp. 2608-2614
    • Brenke, R.1
  • 4
    • 0038526303 scopus 로고    scopus 로고
    • Zdock: An initial-stage protein docking algorithm
    • Chen, R. et al. (2003) Zdock: an initial-stage protein docking algorithm. Proteins, 1, 80-87.
    • (2003) Proteins , vol.1 , pp. 80-87
    • Chen, R.1
  • 5
    • 77951229808 scopus 로고    scopus 로고
    • Fread revisited: Accurate loop structure prediction using a database search algorithm
    • Choi, Y. and Deane, C.M. (2010) Fread revisited: accurate loop structure prediction using a database search algorithm. Proteins, 78, 1431-1440.
    • (2010) Proteins , vol.78 , pp. 1431-1440
    • Choi, Y.1    Deane, C.M.2
  • 6
    • 80755125384 scopus 로고    scopus 로고
    • Predicting antibody complementarity determining region structures without classification
    • Choi, Y. and Deane, C.M. (2011) Predicting antibody complementarity determining region structures without classification. Mol. Biosyst., 7, 3327-3334.
    • (2011) Mol. Biosyst , vol.7 , pp. 3327-3334
    • Choi, Y.1    Deane, C.M.2
  • 7
    • 84891771647 scopus 로고    scopus 로고
    • Sabdab: The structural antibody database
    • Dunbar, J. et al. (2013) Sabdab: the structural antibody database. Nucleic Acids Res., 42, D1140-D1146.
    • (2013) Nucleic Acids Res , vol.42
    • Dunbar, J.1
  • 8
    • 78149293634 scopus 로고    scopus 로고
    • Recent advances in b-cell epitope prediction methods
    • EL-Manzalawy, Y. and Honavar, V. (2010) Recent advances in B-cell epitope prediction methods. Immunome Res., 2, S2.
    • (2010) Immunome Res , vol.2
    • El-Manzalawy, Y.1    Honavar, V.2
  • 9
    • 84884998464 scopus 로고    scopus 로고
    • Antibody i-patch prediction of the antibody binding site improves rigid local antibody-antigen docking
    • Krawczyk, K. et al. (2013) Antibody i-patch prediction of the antibody binding site improves rigid local antibody-antigen docking. Protein Eng. Des. Sel., 26, 621-629.
    • (2013) Protein Eng. Des. Sel , vol.26 , pp. 621-629
    • Krawczyk, K.1
  • 10
    • 84872049601 scopus 로고    scopus 로고
    • Reliable b cell epitope predictions: Impacts of method development and improved benchmarking
    • Kringelum, J.V. et al. (2012) Reliable b cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput. Biol., 8, e1002829.
    • (2012) PLoS Comput. Biol , vol.8
    • Kringelum, J.V.1
  • 11
    • 84867015346 scopus 로고    scopus 로고
    • Computer-aided antibody design
    • Kuroda, D. et al. (2012) Computer-aided antibody design. Protein Eng. Des. Sel., 25, 507-522.
    • (2012) Protein Eng. Des. Sel , vol.25 , pp. 507-522
    • Kuroda, D.1
  • 12
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 13
    • 84884171787 scopus 로고    scopus 로고
    • Prediction of b-cell epitopes using evolutionary information and propensity scales
    • Lin, S.Y. et al. (2013) Prediction of B-cell epitopes using evolutionary information and propensity scales. BMC Bioinformatics, 14, S10.
    • (2013) BMC Bioinformatics , vol.14
    • Lin, S.Y.1
  • 14
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of t4 phage lysozyme
    • Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 15
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of capri predictions in rounds 35 shows progress in docking procedures
    • Mendez, R. et al. (2005) Assessment of capri predictions in rounds 35 shows progress in docking procedures. BMC Bioinformatics, 60, 150-169.
    • (2005) BMC Bioinformatics , vol.60 , pp. 150-169
    • Mendez, R.1
  • 16
    • 85044014155 scopus 로고    scopus 로고
    • Current and experimental antibody-based therapeutics: Insights, breakthroughs, setbacks and future directions
    • Murad, J. et al. (2012) Current and experimental antibody-based therapeutics: insights, breakthroughs, setbacks and future directions. Curr. Mol. Med., 2, 165-178.
    • (2012) Curr. Mol. Med , vol.2 , pp. 165-178
    • Murad, J.1
  • 17
    • 84863246128 scopus 로고    scopus 로고
    • Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens
    • Raghunathan, G. et al. (2012) Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens. J. Mol. Recognit., 25, 103-113.
    • (2012) J. Mol. Recognit , vol.25 , pp. 103-113
    • Raghunathan, G.1
  • 18
    • 84885405356 scopus 로고    scopus 로고
    • The structural basis of antibody-antigen recognition
    • Sela-Culang, I. et al. (2013) The structural basis of antibody-antigen recognition. Front. Immunol., 4, 302.
    • (2013) Front. Immunol , vol.4 , pp. 302
    • Sela-Culang, I.1
  • 19
    • 76749153896 scopus 로고    scopus 로고
    • Snugdock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models
    • Sircar, A. and Gray, J.J. (2010) Snugdock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models. PLoS Comput. Biol., 6, e1000644.
    • (2010) PLoS Comput. Biol , vol.6
    • Sircar, A.1    Gray, J.J.2
  • 20
    • 59449096415 scopus 로고    scopus 로고
    • Toward high-resolution homology modeling of antibody fv regions and application to antibody-antigen docking
    • Sivasubramanian, A. et al. (2009) Toward high-resolution homology modeling of antibody fv regions and application to antibody-antigen docking. Proteins, 74, 497-514.
    • (2009) Proteins , vol.74 , pp. 497-514
    • Sivasubramanian, A.1
  • 21
    • 77955213210 scopus 로고    scopus 로고
    • Use of amino acid composition to predict epitope residues of individual antibodies
    • Soga, S. et al. (2010) Use of amino acid composition to predict epitope residues of individual antibodies. Protein Eng. Des. Sel., 23, 441-448.
    • (2010) Protein Eng. Des. Sel , vol.23 , pp. 441-448
    • Soga, S.1
  • 22
    • 33747356025 scopus 로고    scopus 로고
    • Latest technologies for the enhancement of antibody affinity
    • Wark, K.L. and Hudson, P.J. (2003) Latest technologies for the enhancement of antibody affinity. Adv. Drug Deliv. Rev., 5, 657-670.
    • (2003) Adv. Drug Deliv. Rev , vol.5 , pp. 657-670
    • Wark, K.L.1    Hudson, P.J.2
  • 23
    • 84876426871 scopus 로고    scopus 로고
    • Conformational b-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods
    • Yao, B. et al. (2013) Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One, 8, e62249.
    • (2013) PLoS One , vol.8
    • Yao, B.1
  • 24
    • 77952633690 scopus 로고    scopus 로고
    • Mining for the antibody-antigen interacting associations that predict the b cell epitopes
    • Zhao, L. and Li, J. (2010) Mining for the antibody-antigen interacting associations that predict the b cell epitopes. BMC Struct. Biol., 10, S6.
    • (2010) BMC Struct. Biol , vol.10
    • Zhao, L.1    Li, J.2
  • 25
    • 80052890732 scopus 로고    scopus 로고
    • Antibody-specified b-cell epitope prediction in line with the principle of context-awareness
    • Zhao, L. et al. (2011) Antibody-specified B-cell epitope prediction in line with the principle of context-awareness. IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 1483-1494.
    • (2011) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.8 , pp. 1483-1494
    • Zhao, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.