-
1
-
-
59449096415
-
Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
-
Sivasubramanian, A., Sircar, A., Chaudhury, S. and Gray, J.J. (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins. 74(2):497-514.
-
(2009)
Proteins.
, vol.74
, Issue.2
, pp. 497-514
-
-
Sivasubramanian, A.1
Sircar, A.2
Chaudhury, S.3
Gray, J.J.4
-
2
-
-
76749153896
-
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(1):e1000644.
-
(2010)
PLoS Comput Biol.
, vol.6
, Issue.1
-
-
Sircar, A.1
Gray, J.J.2
-
3
-
-
36749075510
-
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
-
DOI 10.1002/prot.21731
-
Chaudhury, S., Sircar, A., Sivasubramanian, A., Berrondo, M. and Gray, J.J. (2007) Incorporating biochemical information and backbone fl exibility in RosettaDock for CAPRI rounds 6-12. Proteins. 69(4):793-800. (Pubitemid 350210140)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.4
, pp. 793-800
-
-
Chaudhury, S.1
Sircar, A.2
Sivasubramanian, A.3
Berrondo, M.4
Gray, J.J.5
-
4
-
-
77957966065
-
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19
-
Sircar, A., Chaudhury, S., Kilambi, K.P., Berrondo, M. and Gray, J.J. (2010) A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins.
-
(2010)
Proteins
-
-
Sircar, A.1
Chaudhury, S.2
Kilambi, K.P.3
Berrondo, M.4
Gray, J.J.5
-
5
-
-
67849111558
-
RosettaAntibody: Antibody variable region homology modeling server
-
Sircar, A., Kim, E.T. and Gray, J.J. (2009) RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res. 37(Web Server issue):W474-479.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Sircar, A.1
Kim, E.T.2
Gray, J.J.3
-
6
-
-
50549090182
-
PIGS: Automatic prediction of antibody structures
-
Marcatili, P., Rosi, A. and Tramontano, A. (2008) PIGS: automatic prediction of antibody structures. Bioinformatics. 24(17):1953-1954.
-
(2008)
Bioinformatics.
, vol.24
, Issue.17
, pp. 1953-1954
-
-
Marcatili, P.1
Rosi, A.2
Tramontano, A.3
-
7
-
-
0034458999
-
WAM: An improved algorithm for modelling antibodies on the WEB
-
Whitelegg, N.R. and Rees, A.R. (2000) WAM: an improved algorithm for modelling antibodies on the WEB. Protein Eng. 13(12):819-824. (Pubitemid 32233940)
-
(2000)
Protein Engineering
, vol.13
, Issue.12
, pp. 819-824
-
-
Whitelegg, N.R.J.1
Rees, A.R.2
-
8
-
-
84858125431
-
-
Martin, A.C.R. 09/11/2010. How to identify the CDRs by looking at a sequence
-
Martin, A.C.R. 09/11/2010. How to identify the CDRs by looking at a sequence. http:// www.bioinf.org.uk/abs/#cdrid. Accessed 09/11/2010.
-
-
-
-
9
-
-
0004032583
-
-
National Institutes of Health, Bethesda
-
Kabat, E.A., Wu, T.T., Bilofsky, H., Reid-Miller, M. and Perry, H. (1983) Sequence of Proteins of Immunological Interest. National Institutes of Health, Bethesda
-
(1983)
Sequence of Proteins of Immunological Interest
-
-
Kabat, E.A.1
Wu, T.T.2
Bilofsky, H.3
Reid-Miller, M.4
Perry, H.5
-
10
-
-
0031558798
-
Standard conformations for the canonical structures of immunoglobulins
-
DOI 10.1006/jmbi.1997.1354
-
Al-Lazikani, B., Lesk, A.M. and Chothia, C. (1997) Standard conformations for the canonical structures of immunoglobulins. J Mol Biol. 273(4):927-948. (Pubitemid 27493729)
-
(1997)
Journal of Molecular Biology
, vol.273
, Issue.4
, pp. 927-948
-
-
Al-Lazikani, B.1
Lesk, A.M.2
Chothia, C.3
-
11
-
-
48049124972
-
Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
-
Abhinandan, K.R. and Martin, A.C. (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol. 45(14):3832-3839.
-
(2008)
Mol Immunol.
, vol.45
, Issue.14
, pp. 3832-3839
-
-
Abhinandan, K.R.1
Martin, A.C.2
-
12
-
-
0023278330
-
Canonical structures for the hypervariable regions of immunoglobulins
-
Chothia, C. and Lesk, A.M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol. 196(4):901-917. (Pubitemid 17127946)
-
(1987)
Journal of Molecular Biology
, vol.196
, Issue.4
, pp. 901-917
-
-
Chothia, C.1
Lesk, A.M.2
-
13
-
-
0032536197
-
Conformations of the third hypervariable region in the VH domain of immunoglobulins
-
DOI 10.1006/jmbi.1997.1442
-
Morea, V., Tramontano, A., Rustici, M., Chothia, C. and Lesk, A.M. (1998) Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol. 275(2):269-294. (Pubitemid 28030004)
-
(1998)
Journal of Molecular Biology
, vol.275
, Issue.2
, pp. 269-294
-
-
Morea, V.1
Tramontano, A.2
Rustici, M.3
Chothia, C.4
Lesk, A.M.5
-
14
-
-
0030577371
-
Structural classification of CDR-H3 in antibodies
-
DOI 10.1016/S0014-5793(96)01252-5, PII S0014579396012525
-
Shirai, H., Kidera, A. and Nakamura, H. (1996) Structural classifi cation of CDR-H3 in antibodies. FEBS Lett. 399(1-2):1-8. (Pubitemid 27007940)
-
(1996)
FEBS Letters
, vol.399
, Issue.1-2
, pp. 1-8
-
-
Shirai, H.1
Kidera, A.2
Nakamura, H.3
-
15
-
-
0033058759
-
H3-rules: Identification of CDR-H3 structures in antibodies
-
DOI 10.1016/S0014-5793(99)00821-2, PII S0014579399008212
-
Shirai, H., Kidera, A. and Nakamura, H. (1999) H3-rules: identifi cation of CDR-H3 structures in antibodies. FEBS Lett. 455(1-2):188-197. (Pubitemid 29322808)
-
(1999)
FEBS Letters
, vol.455
, Issue.1-2
, pp. 188-197
-
-
Shirai, H.1
Kidera, A.2
Nakamura, H.3
-
16
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res. 28(1):235-242. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
17
-
-
0036171255
-
SACS-Self-maintaining database of antibody crystal structure information
-
Allcorn, L.C. and Martin, A.C. (2002) SACS-self-maintaining database of antibody crystal structure information. Bioinformatics. 18(1):175-181. (Pubitemid 34145046)
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 175-181
-
-
Allcorn, L.C.1
Martin, A.C.R.2
-
18
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-410.
-
(1990)
J Mol Biol.
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
19
-
-
33748988479
-
Long loop prediction using the protein local optimization program
-
DOI 10.1002/prot.21040
-
Zhu, K., Pincus, D.L., Zhao, S. and Friesner, R.A. (2006) Long loop prediction using the protein local optimization program. Proteins. 65(2):438-452. (Pubitemid 44454115)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.2
, pp. 438-452
-
-
Zhu, K.1
Pincus, D.L.2
Zhao, S.3
Friesner, R.A.4
-
20
-
-
68349104348
-
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
-
Mandell, D.J., Coutsias, E.A. and Kortemme, T. (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-552.
-
(2009)
Nat Methods.
, vol.6
, Issue.8
, pp. 551-552
-
-
Mandell, D.J.1
Coutsias, E.A.2
Kortemme, T.3
-
21
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack, R.L., Jr. and Cohen, F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6(8):1661-1681. (Pubitemid 27333069)
-
(1997)
Protein Science
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
22
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
DOI 10.1110/ps.03154503
-
Canutescu, A.A., Shelenkov, A.A. and Dunbrack, R.L., Jr. (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12(9):2001-2014. (Pubitemid 37022822)
-
(2003)
Protein Science
, vol.12
, Issue.9
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack Jr., R.L.3
-
23
-
-
34249777526
-
Eris: An automated estimator of protein stability [2]
-
DOI 10.1038/nmeth0607-466, PII NMETH0607-466
-
Yin, S., Ding, F. and Dokholyan, N.V. (2007) Eris: an automated estimator of protein stability. Nat Methods. 4(6):466-467. (Pubitemid 46852064)
-
(2007)
Nature Methods
, vol.4
, Issue.6
, pp. 466-467
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
24
-
-
33751099863
-
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
-
DOI 10.1110/ps.062405906
-
Haste Andersen, P., Nielsen, M. and Lund, O. (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci. 15(11):2558-2567. (Pubitemid 44771693)
-
(2006)
Protein Science
, vol.15
, Issue.11
, pp. 2558-2567
-
-
Andersen, P.H.1
Nielsen, M.2
Lund, O.3
-
25
-
-
36549031650
-
Pepitope: Epitope mapping from affinity-selected peptides
-
DOI 10.1093/bioinformatics/btm493
-
Mayrose, I., Penn, O., Erez, E., Rubinstein, N.D., Shlomi, T., Freund, N.T., Bublil, E.M., Ruppin, E., Sharan, R., Gershoni, J.M., Martz, E. and Pupko, T. (2007) Pepitope: epitope mapping from affi nity-selected peptides. Bioinformatics. 23(23):3244-3246. (Pubitemid 350187529)
-
(2007)
Bioinformatics
, vol.23
, Issue.23
, pp. 3244-3246
-
-
Mayrose, I.1
Penn, O.2
Erez, E.3
Rubinstein, N.D.4
Shlomi, T.5
Freund, N.T.6
Bublil, E.M.7
Ruppin, E.8
Sharan, R.9
Gershoni, J.M.10
Martz, E.11
Pupko, T.12
-
26
-
-
33747859373
-
RosettaDesign server for protein design
-
DOI 10.1093/nar/gkl163
-
Liu, Y. and Kuhlman, B. (2006) RosettaDesign server for protein design. Nucleic Acids Res. 34(Web Server issue):W235-238. (Pubitemid 44529770)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.WEB. SERV. ISS.
-
-
Liu, Y.1
Kuhlman, B.2
-
27
-
-
79958056394
-
Analysis and modeling of the variable region of camelid single-domain antibodies
-
Sircar, A., Sanni, K.A., Shi, J. and Gray, J.J. Analysis and modeling of the variable region of camelid single-domain antibodies. J Immunol. 186(11):6357-6367.
-
J Immunol.
, vol.186
, Issue.11
, pp. 6357-6367
-
-
Sircar, A.1
Sanni, K.A.2
Shi, J.3
Gray, J.J.4
|