-
1
-
-
0000504484
-
Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure
-
Abagyan, R. and Totrov, M. 1999. Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. J. Comput. Phys. 151: 402-421.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 402-421
-
-
Abagyan, R.1
Totrov, M.2
-
2
-
-
0029018773
-
Ranking potential binding peptides to MHC molecules by a computational threading approach
-
Alluvia, Y., Schueler, O., and Margalit, H. 1995. Ranking potential binding peptides to MHC molecules by a computational threading approach. J. Mol. Biol. 249: 244-250.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 244-250
-
-
Alluvia, Y.1
Schueler, O.2
Margalit, H.3
-
3
-
-
1342268087
-
Analysis and prediction of affinity of TAP binding peptides using cascade SVM
-
Bhasin. M. and Raghava, G.P.S. 2004. Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci. 13: 596-607.
-
(2004)
Protein Sci.
, vol.13
, pp. 596-607
-
-
Bhasin, M.1
Raghava, G.P.S.2
-
4
-
-
0027217789
-
Three-dimensional structure of the human class II histocompatibility antigen HLA-DRI
-
Brown, J.H., Jardetzky, T.S., Gorga, J.C., Stern, L.J., Urban, R.G., Strominger, J.L., and Wiley, D.C. 1993. Three-dimensional structure of the human class II histocompatibility antigen HLA-DRI. Nature 364: 33-39.
-
(1993)
Nature
, vol.364
, pp. 33-39
-
-
Brown, J.H.1
Jardetzky, T.S.2
Gorga, J.C.3
Stern, L.J.4
Urban, R.G.5
Strominger, J.L.6
Wiley, D.C.7
-
5
-
-
0031825709
-
Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
-
1998
-
Brusic, V., Rudy, G., Honeyman, M., Hammer, J., and Harrison, L. 1998. Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. 1998. Bioinformatics 14: 121-130.
-
(1998)
Bioinformatics
, vol.14
, pp. 121-130
-
-
Brusic, V.1
Rudy, G.2
Honeyman, M.3
Hammer, J.4
Harrison, L.5
-
6
-
-
0035989339
-
Prediction of promiscuous peptides that bind HLA class I molecules
-
Brusic, V., Petrovsky, N., Zhang, G., and Bajic, V.B. 2002. Prediction of promiscuous peptides that bind HLA class I molecules, Immunol. Cell Biol. 80: 280-285.
-
(2002)
Immunol. Cell Biol.
, vol.80
, pp. 280-285
-
-
Brusic, V.1
Petrovsky, N.2
Zhang, G.3
Bajic, V.B.4
-
7
-
-
0026721978
-
Monte Carlo docking of oligopeptides to proteins
-
Caflisch, A., Niederer, P., and Anliker, M. 1992. Monte Carlo docking of oligopeptides to proteins. Proteins 13: 223-230.
-
(1992)
Proteins
, vol.13
, pp. 223-230
-
-
Caflisch, A.1
Niederer, P.2
Anliker, M.3
-
8
-
-
0029125234
-
An empirical method for the prediction of T-cell epitopes
-
Davenport, M.P., Ho Shon, I., and Hill, A.V. 1995. An empirical method for the prediction of T-cell epitopes. Immunogenetics 42: 392-397.
-
(1995)
Immunogenetics
, vol.42
, pp. 392-397
-
-
Davenport, M.P.1
Ho Shon, I.2
Hill, A.V.3
-
9
-
-
0034566932
-
Flexible docking of peptide ligands to proteins
-
Desmet, J., Maeyer, M.D., Spriet, J., and Lasters, I. 2000. Flexible docking of peptide ligands to proteins. Methods Mol. Biol. 143: 359-376.
-
(2000)
Methods Mol. Biol.
, vol.143
, pp. 359-376
-
-
Desmet, J.1
Maeyer, M.D.2
Spriet, J.3
Lasters, I.4
-
10
-
-
0142174642
-
Prediction of MHC class I binding peptides, using SVMHC
-
Dönnes, P. and Elofsson, A. 2002. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3: 1-8.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 1-8
-
-
Dönnes, P.1
Elofsson, A.2
-
11
-
-
0025855156
-
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
-
Falk, K., Rotzschke, O., Stevanovic, S., Jung, G., and Rammensee, H.G. 1991. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351: 290-296.
-
(1991)
Nature
, vol.351
, pp. 290-296
-
-
Falk, K.1
Rotzschke, O.2
Stevanovic, S.3
Jung, G.4
Rammensee, H.G.5
-
12
-
-
0036149480
-
Soft protein-protein docking in internal coordinates
-
Fernández-Recio, J., Totrov, M., and Abagyan, R. 2002. Soft protein-protein docking in internal coordinates. Protein Sci. 11: 280-291.
-
(2002)
Protein Sci.
, vol.11
, pp. 280-291
-
-
Fernández-Recio, J.1
Totrov, M.2
Abagyan, R.3
-
13
-
-
0038796566
-
Databases and data mining for computational vaccinology
-
Flower, D.R. 2003. Databases and data mining for computational vaccinology. Curr. Opin. Drug Discov. Devel. 6: 396-400.
-
(2003)
Curr. Opin. Drug Discov. Devel.
, vol.6
, pp. 396-400
-
-
Flower, D.R.1
-
14
-
-
0032528495
-
Use of complete eluted peptide sequence data from HLA-DR and -DQ molecules to predict T cell epitopes and the influence of the nonbinding terminal regions of ligands in epitope selection
-
Godkin, A.J., Davenport, M.P., Willis, A., Jewell, D.P., and Hill, A.V. 1998. Use of complete eluted peptide sequence data from HLA-DR and -DQ molecules to predict T cell epitopes and the influence of the nonbinding terminal regions of ligands in epitope selection. J. Immunol. 161: 850-858.
-
(1998)
J. Immunol.
, vol.161
, pp. 850-858
-
-
Godkin, A.J.1
Davenport, M.P.2
Willis, A.3
Jewell, D.P.4
Hill, A.V.5
-
15
-
-
0037314055
-
MPID: MHC-peptide interaction database for sequence-structure-function information on peptides binding to MHC molecules
-
Govindarajan, K.R., Kangueane, P., Tan, T.W., and Ranganathan, S. 2003. MPID: MHC-peptide interaction database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics 19: 309-310.
-
(2003)
Bioinformatics
, vol.19
, pp. 309-310
-
-
Govindarajan, K.R.1
Kangueane, P.2
Tan, T.W.3
Ranganathan, S.4
-
16
-
-
0031576987
-
Two complementary methods for predicting peptides binding major histocompatibility complex molecules
-
Gulukota, K., Sidney. J., Sette, A., and DeLisi, C. 1997. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol. 267: 1258-1267.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1258-1267
-
-
Gulukota, K.1
Sidney, J.2
Sette, A.3
DeLisi, C.4
-
17
-
-
0026618817
-
Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle
-
Guo, H.C., Jardetzky, T.S., Garrett, T.P.J., Lane, W.S., Strominger, J.L., and Wiley, D.C. 1992. Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Nature 360: 364-366.
-
(1992)
Nature
, vol.360
, pp. 364-366
-
-
Guo, H.C.1
Jardetzky, T.S.2
Garrett, T.P.J.3
Lane, W.S.4
Strominger, J.L.5
Wiley, D.C.6
-
19
-
-
0029926327
-
Selection of peptides that bind to the HLA-A2.1 molecule by molecular modeling
-
Lim, S.K., Kim, S., Lee, H.G., Lee, K.Y., Kwon, T.J., and Kim, K. 1996. Selection of peptides that bind to the HLA-A2.1 molecule by molecular modeling. Mol. Immunol. 33: 221-230.
-
(1996)
Mol. Immunol.
, vol.33
, pp. 221-230
-
-
Lim, S.K.1
Kim, S.2
Lee, H.G.3
Lee, K.Y.4
Kwon, T.J.5
Kim, K.6
-
20
-
-
0032387825
-
Predicting peptides that bind to MHC molecules using supervised learning of Hidden Markov Models
-
Mamitsuka, H. 1998. Predicting peptides that bind to MHC molecules using supervised learning of Hidden Markov Models. Proteins 33: 460-474.
-
(1998)
Proteins
, vol.33
, pp. 460-474
-
-
Mamitsuka, H.1
-
21
-
-
0036447407
-
Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: A stimulation analysis
-
Michielin, O. and Karplus, M. 2002. Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: A stimulation analysis. J. Mol. Biol. 324: 547-569.
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 547-569
-
-
Michielin, O.1
Karplus, M.2
-
22
-
-
0034725455
-
Modeling the TCR-MHC-peptide complex
-
Michielin, O., Luescher, I., and Karplus, M. 2000. Modeling the TCR-MHC-peptide complex. J. Mol. Biol. 300: 1205-1235.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1205-1235
-
-
Michielin, O.1
Luescher, I.2
Karplus, M.3
-
23
-
-
0001731773
-
Energy parameters in polypeptides, 10: Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to praline-containing peptides
-
Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H.A. 1992. Energy parameters in polypeptides, 10: Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to praline-containing peptides. J. Phys. Chem. 96: 6472-6484.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 6472-6484
-
-
Nemethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
24
-
-
0028052724
-
Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains
-
Parker, K.C., Bednarek, M.A., and Coligan, I.E. 1994. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J. Immunol. 152: 163-175.
-
(1994)
J. Immunol.
, vol.152
, pp. 163-175
-
-
Parker, K.C.1
Bednarek, M.A.2
Coligan, I.E.3
-
25
-
-
0033388725
-
SYFPEITHI: Database for MHC ligands and peptide motifs
-
Rammensee, H., Bachmann, J., Emmerich, N.P., Bachor, O.A., and Stevanović, S. 1999. SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics 50: 213-219.
-
(1999)
Immunogenetics
, vol.50
, pp. 213-219
-
-
Rammensee, H.1
Bachmann, J.2
Emmerich, N.P.3
Bachor, O.A.4
Stevanović, S.5
-
26
-
-
0033523959
-
Predicting binding affinities of protein ligands from three-dimensional models: Application to peptide binding to class I major histocompatibility proteins
-
Rognan, D., Laumoeller, S.L., Holm, A., Buus, S., and Tschinke, V. 1999. Predicting binding affinities of protein ligands from three-dimensional models: Application to peptide binding to class I major histocompatibility proteins. J. Med. Chem. 42: 4650-4658.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 4650-4658
-
-
Rognan, D.1
Laumoeller, S.L.2
Holm, A.3
Buus, S.4
Tschinke, V.5
-
27
-
-
0027135804
-
Computing the structure of bound peptides: Application to antigen recognition by class I major histocompatibility complex receptors
-
Rosenfeld, R., Zheng, Q., Vajda, S., and DeLisi, C. 1993. Computing the structure of bound peptides: Application to antigen recognition by class I major histocompatibility complex receptors. J. Mol. Biol. 234: 515-521.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 515-521
-
-
Rosenfeld, R.1
Zheng, Q.2
Vajda, S.3
DeLisi, C.4
-
28
-
-
4344629312
-
Flexible docking of peptides to class I major-histocompatibility-complex receptors
-
-. 1995. Flexible docking of peptides to class I major- histocompatibility-complex receptors. Genet. Anal. 12: 1-21.
-
(1995)
Genet. Anal.
, vol.12
, pp. 1-21
-
-
-
29
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
30
-
-
0029975683
-
Free energy mapping of class I MHC molecules and structural determination of bound peptides
-
Sezerman, U., Vajda, S., and DeLisi, C. 1996. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci. 5: 1272-1281.
-
(1996)
Protein Sci.
, vol.5
, pp. 1272-1281
-
-
Sezerman, U.1
Vajda, S.2
DeLisi, C.3
-
31
-
-
0028773294
-
Antigenic peptide binding by class I and class II histocompatibility proteins
-
Stern, L.J. and Wiley, D.C. 1994. Antigenic peptide binding by class I and class II histocompatibility proteins. Structure 2: 245-251.
-
(1994)
Structure
, vol.2
, pp. 245-251
-
-
Stern, L.J.1
Wiley, D.C.2
-
32
-
-
0028348369
-
Crystal structure of the human class II MHC protein HLA-DRI complexed with an influenza virus peptide
-
Stern, L.J., Brown, J.H., Jardetzky, T.S., Gorga, J.C., Urban, R.G., Strominger, J.L., and Wiley, D.C. 1994. Crystal structure of the human class II MHC protein HLA-DRI complexed with an influenza virus peptide. Nature 368: 215-221.
-
(1994)
Nature
, vol.368
, pp. 215-221
-
-
Stern, L.J.1
Brown, J.H.2
Jardetzky, T.S.3
Gorga, J.C.4
Urban, R.G.5
Strominger, J.L.6
Wiley, D.C.7
|