-
1
-
-
0031925498
-
Recent advances in structure-based ligand design using molecular dynamics and Monte Carlo methods
-
Kollman, P. Recent advances in structure-based ligand design using molecular dynamics and Monte Carlo methods. Pharm. Res. 1998, 15, 368-370.
-
(1998)
Pharm. Res.
, vol.15
, pp. 368-370
-
-
Kollman, P.1
-
2
-
-
2542564912
-
Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules
-
Kollman, P. A. Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc. Chem. Res. 1996, 29, 461-469.
-
(1996)
Acc. Chem. Res.
, vol.29
, pp. 461-469
-
-
Kollman, P.A.1
-
3
-
-
0027321958
-
Absolute and relative binding free energy calculations of the interaction of biotin and its analogues with streptavidin using molecular dynamics/free energy perturbation approaches
-
Miyamoto, S.; Kollman, P. A. Absolute and relative binding free energy calculations of the interaction of biotin and its analogues with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins 1993, 16, 226-245.
-
(1993)
Proteins
, vol.16
, pp. 226-245
-
-
Miyamoto, S.1
Kollman, P.A.2
-
4
-
-
0027239578
-
What determines the strength of noncovalent association of ligands to proteins in aqueous solution?
-
Miyamoto, S.; Kollman, P. A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc. Natl. Acad. Sci. U.SA. 1993, 90, 8402-8406.
-
(1993)
Proc. Natl. Acad. Sci. U.SA.
, vol.90
, pp. 8402-8406
-
-
Miyamoto, S.1
Kollman, P.A.2
-
5
-
-
0032054675
-
Computational alchemy to calculate absolute protein-ligand binding free energy
-
Helms, V.; Wade, R. Computational alchemy to calculate absolute protein-ligand binding free energy. J. Am. Chem. Soc. 1998, 720, 2710-2713.
-
(1998)
J. Am. Chem. Soc.
, vol.720
, pp. 2710-2713
-
-
Helms, V.1
Wade, R.2
-
6
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm, H. J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
-
(1994)
J. Comput.-aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.J.1
-
7
-
-
0032112137
-
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
-
Böhm, H. J. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J. Comput.-Aided Mol. Des. 1998, 12, 309-323.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 309-323
-
-
Böhm, H.J.1
-
8
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M.; Murray, C. W.; Auton, T. A.; Paolini, G. V.; Lee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.1
Murray, C.W.2
Auton, T.A.3
Paolini, G.V.4
Lee, R.P.5
-
9
-
-
0032153192
-
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of bayesian regression to improve the quality of the model
-
Murray, C. W.; Auton, T. A.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. J. Comput.-Aided Mol. Des. 1998, 12, 503-519.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 503-519
-
-
Murray, C.W.1
Auton, T.A.2
Eldridge, M.D.3
-
10
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Åqvist, J. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 1994, 7, 385-391.
-
(1994)
Protein Eng.
, vol.7
, pp. 385-391
-
-
Åqvist, J.1
-
11
-
-
0029063951
-
A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site
-
Holloway, M. K.; Wai, J. M.; Halgren, T. A.; Fitzgerald, P. M.; Vacca, J. P.; Dorsey, B. D.; Levin, R. B.; Thompson, W. J.; Chen, L. J.; deSolms, S. J. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site J. Med. Chem. 1995, 38, 305-317.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 305-317
-
-
Holloway, M.K.1
Wai, J.M.2
Halgren, T.A.3
Fitzgerald, P.M.4
Vacca, J.P.5
Dorsey, B.D.6
Levin, R.B.7
Thompson, W.J.8
Chen, L.J.9
DeSolms, S.J.10
-
12
-
-
0027139338
-
Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures
-
Krystek, S.; Stouch, T.; Novotny, J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. J. Mol. Biol. 1993, 234, 661-679.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 661-679
-
-
Krystek, S.1
Stouch, T.2
Novotny, J.3
-
13
-
-
0032486764
-
Designing an optimal guest for a host using multimolecule free energy calculations: Predicting the best ligand for Rebek's "tennis ball"
-
Pitera, J.; Kollman, P. A. Designing an optimal guest for a host using multimolecule free energy calculations: Predicting the best ligand for Rebek's "Tennis Ball" J. Am. Chem. Soc. 1998, 120, 7557-7567.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 7557-7567
-
-
Pitera, J.1
Kollman, P.A.2
-
14
-
-
0029135744
-
Pseudoreceptor modeling: A new concept for the three-dimensional construction of receptor binding sites
-
Vedani, A.; Zbinden, P.; Snyder, J. P.; Greenidge, P. Pseudoreceptor modeling: A new concept for the three-dimensional construction of receptor binding sites. J. Am. Chem. Soc. 1995, 117, 4987-4994.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4987-4994
-
-
Vedani, A.1
Zbinden, P.2
Snyder, J.P.3
Greenidge, P.4
-
15
-
-
0023751431
-
Comparative molecular field analysis (CoMFA). I. Effect of shape on binding of steroids to carrier proteins
-
Cramer, R. D. I.; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). I. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5959-5967
-
-
Cramer, R.D.I.1
Patterson, D.E.2
Bunce, J.D.3
-
16
-
-
0029995624
-
Validate: A new method for the receptor-based prediction of binding affinities of novel ligands
-
Head, H. J.; Smythe, M. L.; Oprea, T. I.; Waller, C. L.; Green, S. M.; Marshall, G. A. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands J. Am. Chem. Soc. 1996, 118, 3959-3969.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 3959-3969
-
-
Head, H.J.1
Smythe, M.L.2
Oprea, T.I.3
Waller, C.L.4
Green, S.M.5
Marshall, G.A.6
-
17
-
-
0030021877
-
Computational method for relative binding energies of enzyme-substrate complexes
-
Zhang, T.; Koshland, D. E. J. Computational method for relative binding energies of enzyme-substrate complexes. Protein Sci. 1996, 5, 348-356.
-
(1996)
Protein Sci.
, vol.5
, pp. 348-356
-
-
Zhang, T.1
Koshland, D.E.J.2
-
18
-
-
84986440390
-
Calculation of binding energy differences for receptor-ligand systems using the Poisson-Boltzmann method
-
Shen, J.; Quiocho, F. A. Calculation of binding energy differences for receptor-ligand systems using the Poisson-Boltzmann method. J. Comput. Chem. 1995, 16, 445-448.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 445-448
-
-
Shen, J.1
Quiocho, F.A.2
-
19
-
-
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.; Wiley, D. C. Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Nature 1992, 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
-
20
-
-
0027525106
-
The antigenic identity of peptide/MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2
-
Madden, D. R.; Garboczi, D. N.; Wiley: D. C. The antigenic identity of peptide/MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell 1993, 75, 693-708.
-
(1993)
Cell
, vol.75
, pp. 693-708
-
-
Madden, D.R.1
Garboczi, D.N.2
Wiley, D.C.3
-
21
-
-
0026721978
-
Monte Carlo docking of oligopeptides to proteins
-
Caflisch, A.; Niederer, P.; Anliker, P. Monte Carlo docking of oligopeptides to proteins. Proteins 1992, 13, 223-230.
-
(1992)
Proteins
, vol.13
, pp. 223-230
-
-
Caflisch, A.1
Niederer, P.2
Anliker, P.3
-
22
-
-
0026646376
-
Molecular dynamics study of a complex between the human histocompatibility antigen HLA-A2 and the IMP58-66 nonapeptide from influenza virus matrix protein
-
Rognan, D.; Zimmermann, A.; Jung, J.; Folkers, G. Molecular dynamics study of a complex between the human histocompatibility antigen HLA-A2 and the IMP58-66 nonapeptide from influenza virus matrix protein. Eur. J. Biochem. 1992, 208, 101-113.
-
(1992)
Eur. J. Biochem.
, vol.208
, pp. 101-113
-
-
Rognan, D.1
Zimmermann, A.2
Jung, J.3
Folkers, G.4
-
23
-
-
0027491716
-
Toward computational determination of peptide-receptor structure
-
Sezerman, U.; Vajda, S.; Cornette, J.; DeLisi, C. Toward computational determination of peptide-receptor structure. Protein Sci. 1993, 2, 1827-1843.
-
(1993)
Protein Sci.
, vol.2
, pp. 1827-1843
-
-
Sezerman, U.1
Vajda, S.2
Cornette, J.3
DeLisi, C.4
-
24
-
-
0000895361
-
Peptide docking using dynamic programming
-
Gulukota, K.; Vajda, S.; DeLisi, C. Peptide docking using dynamic programming. J. Comput. Chem. 1996, 17, 418-428.
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 418-428
-
-
Gulukota, K.1
Vajda, S.2
DeLisi, C.3
-
25
-
-
0027135804
-
Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors
-
Rosenfeld, R.; Zheng, Q.; Vajda, S.; DeLisi, C. Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors. J. Mol. Biol. 1993, 234, 515-521.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 515-521
-
-
Rosenfeld, R.1
Zheng, Q.2
Vajda, S.3
DeLisi, C.4
-
26
-
-
0029975683
-
Free energy mapping of class I MHC molecules and structural determination of bound peptides
-
Sezerman, U.; Vajda, S.; DeLisi, C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci. 1996, 5, 1271-1281.
-
(1996)
Protein Sci.
, vol.5
, pp. 1271-1281
-
-
Sezerman, U.1
Vajda, S.2
DeLisi, C.3
-
27
-
-
0029018773
-
Ranking potential binding peptides to MHC molecules by a computational threading approach
-
Altuvia, Y.; Schueler, O.; Margalit, H. Ranking potential binding peptides to MHC molecules by a computational threading approach. J. Mol. Biol. 1995, 249, 244-250.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 244-250
-
-
Altuvia, Y.1
Schueler, O.2
Margalit, H.3
-
28
-
-
0031455540
-
A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets
-
Altuvia, Y.; Sette, A.; Sidney, J.; Southwood, S.; Margalit, H. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum. Immunol. 1997, 58, 1-11.
-
(1997)
Hum. Immunol.
, vol.58
, pp. 1-11
-
-
Altuvia, Y.1
Sette, A.2
Sidney, J.3
Southwood, S.4
Margalit, H.5
-
29
-
-
0032441130
-
Knowledge-based structure prediction of MHC class i bound peptides: A study of 23 complexes
-
Schueler-Furman, O.; Elber, R.; Margalit, H. Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes. Folding Des. 1998, 3, 549-564.
-
(1998)
Folding Des.
, vol.3
, pp. 549-564
-
-
Schueler-Furman, O.1
Elber, R.2
Margalit, H.3
-
30
-
-
0031008575
-
On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide complexes
-
Froloff, N.; Windemuth, A.; Honig, B. On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide complexes. Protein Sci. 1997, 6, 1293-1301.
-
(1997)
Protein Sci.
, vol.6
, pp. 1293-1301
-
-
Froloff, N.1
Windemuth, A.2
Honig, B.3
-
31
-
-
0031868557
-
Toward a predictive understanding of molecular recognition
-
Weng, Z.; DeLisi, C. Toward a predictive understanding of molecular recognition. Immunol. Rev. 1998, 163, 251-266.
-
(1998)
Immunol. Rev.
, vol.163
, pp. 251-266
-
-
Weng, Z.1
DeLisi, C.2
-
32
-
-
0030945036
-
Consistency in structural energetics of protein folding and recognition
-
Zhang, C.; Cornette, J. L.; DeLisi, C. Consistency in structural energetics of protein folding and recognition. Protein Sci. 1997, 6, 1057-1064.
-
(1997)
Protein Sci.
, vol.6
, pp. 1057-1064
-
-
Zhang, C.1
Cornette, J.L.2
DeLisi, C.3
-
33
-
-
0024324442
-
Association of class I major histocompatibility heavy and light chains induced by viral peptides
-
Townsend, A.; Ohlen, C.; Bastin, J.; Ljunggren, H. G.; Foster, L.; Karre, K. Association of class I major histocompatibility heavy and light chains induced by viral peptides. Nature 1989, 340, 443-448.
-
(1989)
Nature
, vol.340
, pp. 443-448
-
-
Townsend, A.1
Ohlen, C.2
Bastin, J.3
Ljunggren, H.G.4
Foster, L.5
Karre, K.6
-
34
-
-
0028131363
-
Importance of peptide amino and carboxy termini to the stability of MHC class I molecules
-
Bouvier, M.; Wiley: D. C. Importance of peptide amino and carboxy termini to the stability of MHC class I molecules. Science 1994, 265, 398-402.
-
(1994)
Science
, vol.265
, pp. 398-402
-
-
Bouvier, M.1
Wiley, D.C.2
-
35
-
-
0029118267
-
HLA class i nucleotide sequences, 1995
-
Arnett, K. L.; Parham, P. HLA class I nucleotide sequences, 1995. Tissue Antigens 1995, 46, 217-257.
-
(1995)
Tissue Antigens
, vol.46
, pp. 217-257
-
-
Arnett, K.L.1
Parham, P.2
-
36
-
-
0028845419
-
Differences in MHC class i self-peptide repertoires among HLA-A2 subtypes
-
Sudo, T.; Kamikawaji, N.; Kimura, A.; Date, Y.; Savoie, C. J.; Nakashima, H.; Furuichi, E.; Kuhara, S.; Sasazuki, T. Differences in MHC class I self-peptide repertoires among HLA-A2 subtypes. J. Immunol. 1995, 155, 4749-4756.
-
(1995)
J. Immunol.
, vol.155
, pp. 4749-4756
-
-
Sudo, T.1
Kamikawaji, N.2
Kimura, A.3
Date, Y.4
Savoie, C.J.5
Nakashima, H.6
Furuichi, E.7
Kuhara, S.8
Sasazuki, T.9
-
37
-
-
0029662223
-
An αβ T cell receptor structure at 2.5 a and its orientation in the TCR-MHC complex
-
Garcia, K C.; Degano, M.; Stanfield, R. L.; Brunmark, A.; Jackson, M. R.; Peterson, P. A.: Teyton, L.; Wilson, I. A. An αβ T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science 1996, 274, 209-219.
-
(1996)
Science
, vol.274
, pp. 209-219
-
-
Garcia, K.C.1
Degano, M.2
Stanfield, R.L.3
Brunmark, A.4
Jackson, M.R.5
Peterson, P.A.6
Teyton, L.7
Wilson, I.A.8
-
38
-
-
0029855347
-
Structure of the complex between human T-cell receptor, viral peptide and HLA-A2
-
Garboczi, D. N.; Ghosh, P.; Utz, U.; Fan, Q. R.; Biddison, W. E.; Wiley, D. C. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 1986, 384, 134-141.
-
(1986)
Nature
, vol.384
, pp. 134-141
-
-
Garboczi, D.N.1
Ghosh, P.2
Utz, U.3
Fan, Q.R.4
Biddison, W.E.5
Wiley, D.C.6
-
39
-
-
0032549142
-
Structural basis of plasticity in T cell receptor recognition of a self-peptide-MHC antigen
-
Garcia, K. C.; Degano, M.; Pease, L. R.; Huang, M.; Peterson, P. A.; Teyton, L.; Wilson, I. A. Structural basis of plasticity in T cell receptor recognition of a self-peptide-MHC antigen. Science 1998, 279, 1666-1672.
-
(1998)
Science
, vol.279
, pp. 1666-1672
-
-
Garcia, K.C.1
Degano, M.2
Pease, L.R.3
Huang, M.4
Peterson, P.A.5
Teyton, L.6
Wilson, I.A.7
-
40
-
-
0027304399
-
Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules
-
Ruppert, J.; Sidney, J.; Cells, E.; Kubo, R. T.; Grey, H. M.; Sette, A. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 1993, 74, 929-37.
-
(1993)
Cell
, vol.74
, pp. 929-937
-
-
Ruppert, J.1
Sidney, J.2
Cells, E.3
Kubo, R.T.4
Grey, H.M.5
Sette, A.6
-
41
-
-
0031307020
-
Competitive assessment of protein fold recognition and alignment accuracy
-
Levitt, M. Competitive assessment of protein fold recognition and alignment accuracy. Proteins 1997, 1, 92-104.
-
(1997)
Proteins
, vol.1
, pp. 92-104
-
-
Levitt, M.1
-
42
-
-
0000136289
-
Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution
-
Saper, M. A.; Bjorkman, P. J.; Wiley, D. C. Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution. J. Mol. Biol. 1991, 75, 693-708.
-
(1991)
J. Mol. Biol.
, vol.75
, pp. 693-708
-
-
Saper, M.A.1
Bjorkman, P.J.2
Wiley, D.C.3
-
43
-
-
0026794581
-
The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC
-
Madden, D. R.; Gorga, J. C.; Strominger, J. L.; Wiley: D. C. The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Cell 1992, 70, 1035-1048.
-
(1992)
Cell
, vol.70
, pp. 1035-1048
-
-
Madden, D.R.1
Gorga, J.C.2
Strominger, J.L.3
Wiley, D.C.4
-
44
-
-
0025855156
-
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
-
Falk, K.; Rötzschke, O.; Stevanovic, S.; Jung, G.; Rammensee, H.-G. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991, 351, 290-296.
-
(1991)
Nature
, vol.351
, pp. 290-296
-
-
Falk, K.1
Rötzschke, O.2
Stevanovic, S.3
Jung, G.4
Rammensee, H.-G.5
-
45
-
-
0028987213
-
Crystal structure of an h-2kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove
-
Fremont, D. H.; Stura, E. A.; Matsumura, M.; Peterson, P. A.; Wilson, I. A. Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove Proc. Natl. Acad. Sci. U.S.A. 1985, 92, 2479-83.
-
(1985)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 2479-2483
-
-
Fremont, D.H.1
Stura, E.A.2
Matsumura, M.3
Peterson, P.A.4
Wilson, I.A.5
-
46
-
-
0030760565
-
Peptide binding by class I and class II MHC molecules
-
Batalia, M. A.; Collins, E. J. Peptide binding by class I and class II MHC molecules. Biopolymers 1997, 43, 281-302.
-
(1997)
Biopolymers
, vol.43
, pp. 281-302
-
-
Batalia, M.A.1
Collins, E.J.2
-
47
-
-
9444240941
-
Peptide binding specificity of major histocompatibility complex class i resolved into an array of apparently independent subspecificities. Quantitation by peptide libraries and improved prediction of binding
-
Stryhn, A.; Pedersen, L. O.; Romme, T.; Holm, C. B.; Holm, A.; Buus, S. Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities. quantitation by peptide libraries and improved prediction of binding. Eur. J. Immunol. 1996, 26, 1911-1918.
-
(1996)
Eur. J. Immunol.
, vol.26
, pp. 1911-1918
-
-
Stryhn, A.1
Pedersen, L.O.2
Romme, T.3
Holm, C.B.4
Holm, A.5
Buus, S.6
-
48
-
-
0029814159
-
Shared fine specificity between t-cell receptors and an antibody recognizing a peptide/major histocompatibility class i complex
-
Stryhn, A.; Andersen, P. S.; Pedersen, L. O.; Svejgaard, A.; Holm, A.; Thorpe, C. J.; Fugger, L.; Buus, S.; Engberg, J. Shared fine specificity between T-cell receptors and an antibody recognizing a peptide/major histocompatibility class I complex. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10338-10342.
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 10338-10342
-
-
Stryhn, A.1
Andersen, P.S.2
Pedersen, L.O.3
Svejgaard, A.4
Holm, A.5
Thorpe, C.J.6
Fugger, L.7
Buus, S.8
Engberg, J.9
-
49
-
-
0033118895
-
Description and prediction of MHC-binding motifs: The "human MHC project"
-
Buus, S. Description and prediction of MHC-binding motifs: the "human MHC project". Curr. Opin. Immunol. 1999, 11, 209-213.
-
(1999)
Curr. Opin. Immunol.
, vol.11
, pp. 209-213
-
-
Buus, S.1
-
50
-
-
0031576987
-
Two complementary methods for predicting peptides binding major histocompatibility complex molecules
-
Gulukota, K.; Sidney, J.; Sette, A.; DeLisi, C. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol. 1997, 267, 1258-1267.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1258-1267
-
-
Gulukota, K.1
Sidney, J.2
Sette, A.3
DeLisi, C.4
-
51
-
-
0031760687
-
Neural network-based prediction of candidate t-cell epitopes
-
Honeyman, M. C.; Brusic, V.; Stone, N. L.; Harrison, L. C. Neural network-based prediction of candidate T-cell epitopes. Nature Biotechnol. 1998, 16, 966-969
-
(1998)
Nature Biotechnol.
, vol.16
, pp. 966-969
-
-
Honeyman, M.C.1
Brusic, V.2
Stone, N.L.3
Harrison, L.C.4
-
52
-
-
0028052724
-
Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains
-
Parker, K. C, Bednarek, M. A, Coligan, J. E. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J. Immunol. 1994, 152, 163-175.
-
(1994)
J. Immunol.
, vol.152
, pp. 163-175
-
-
Parker, K.C.1
Bednarek, M.A.2
Coligan, J.E.3
-
53
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. M.; Kennard, O.; Shimanouchi, T. M. T. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 1977, 112, 537-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 537-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.J.4
Brice, M.D.5
Rodgers, J.M.6
Kennard, O.7
Shimanouchi, T.M.T.8
-
54
-
-
0028135684
-
Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes
-
Rognan, D.; Scapozza, L.; Folkers, G.; Daser, A. Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochemistry 1994, 33, 11476-11485.
-
(1994)
Biochemistry
, vol.33
, pp. 11476-11485
-
-
Rognan, D.1
Scapozza, L.2
Folkers, G.3
Daser, A.4
-
55
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids and organic molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, J., K. M.; Ferguson, D. M.; Spellmeyer, D. M.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, J.K.M.5
Ferguson, D.M.6
Spellmeyer, D.M.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
56
-
-
0003700434
-
-
University of California: San Francisco
-
Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham III, T. E.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 5.0; University of California: San Francisco, 1997.
-
(1997)
AMBER 5.0
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham T.E. III4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Ferguson, D.M.13
Radmer, R.J.14
Seibel, G.L.15
Singh, U.C.16
Weiner, P.K.17
Kollman, P.A.18
-
57
-
-
85135598468
-
Modelling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two αβ T cell receptors
-
in press
-
Rognan, D.; Stryhn, A.; Fugger, L.; Lynbaeck, S.; Engberg, J.; Andersen, P. S.; Buus, S. Modelling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two αβ T cell receptors. J. Comput.-Aided Mol. Des. 1999, in press.
-
(1999)
J. Comput.-aided Mol. Des.
-
-
Rognan, D.1
Stryhn, A.2
Fugger, L.3
Lynbaeck, S.4
Engberg, J.5
Andersen, P.S.6
Buus, S.7
-
58
-
-
0001658242
-
An empirical examination of potential energy minimization using the well-determined structure of the protein crambin
-
Whitlow, M.; Teeter, M. M. An empirical examination of potential energy minimization using the well-determined structure of the protein crambin. J. Am. Chem. Soc. 1986, 108, 71-64-7172.
-
(1986)
J. Am. Chem. Soc.
, vol.108
, pp. 7164-7172
-
-
Whitlow, M.1
Teeter, M.M.2
-
59
-
-
84986518987
-
Molecular docking using shape descritors
-
Meng, E. C., Stoichet, B. K., Kuntz, I. D. Molecular docking using shape descritors. J. Comput. Chem. 1992, 13, 380-397.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 380-397
-
-
Meng, E.C.1
Stoichet, B.K.2
Kuntz, I.D.3
-
60
-
-
20544433165
-
Waals volumes and radii
-
Bondi, A. van der Waals volumes and radii. J. Phys. Chem. 1964, 68, 441-451.
-
(1964)
J. Phys. Chem.
, vol.68
, pp. 441-451
-
-
Van Bondi, A.D.1
-
61
-
-
0344045232
-
-
note
-
The choice of the van der Waals radii influences the value of the lipophilic, buried-polar, and rotational terms. In the present work we use the following van der Waals radii in angstroms: H, 1.20; C, 1.70; N, 1.55; O, 1.52; F, 1.47; P, 1.80; S, 1.80; Cl, 1.75; Br, 1.85; I, 1.80.
-
-
-
-
62
-
-
0020475509
-
Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
-
Warwicker, J.; Watson, H. C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 1982, 757, 671.
-
(1982)
J. Mol. Biol.
, vol.757
, pp. 671
-
-
Warwicker, J.1
Watson, H.C.2
-
63
-
-
0022964504
-
Focusing of electric fields in the active site of cu-zn superoxide dismutase: Effects of ionic strength and amino acid modification
-
Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Focusing of electric fields in the active site of Cu-Zn Superoxide dismutase: effects of ionic strength and amino acid modification. Proteins 1986, 1, 47-59.
-
(1986)
Proteins
, vol.1
, pp. 47-59
-
-
Klapper, I.1
Hagstrom, R.2
Fine, R.3
Sharp, K.4
Honig, B.5
-
64
-
-
0030157593
-
A structural and energetics analysis of the binding of a series of N-acetylneuramic-acid-based inhibitors to influenza virus sialidase
-
Taylor, N. R.; von Iztein, M. A structural and energetics analysis of the binding of a series of N-acetylneuramic-acid-based inhibitors to influenza virus sialidase. J. Comput.-Aided Mol. Des. 1996, 10, 233-246.
-
(1996)
J. Comput.-Aided Mol. Des.
, vol.10
, pp. 233-246
-
-
Taylor, N.R.1
Von Iztein, M.2
-
65
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson, M. K.; Honig, B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988, 4, 7-18.
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
66
-
-
84988087911
-
Calculating electrostatic interactions in bio-molecules: Method and error assessment
-
Gilson, M. K.; Sharp, K.; Honig, B. Calculating electrostatic interactions in bio-molecules: Method and error assessment. J. Comput. Chem. 1988, 9, 327-335.
-
(1988)
J. Comput. Chem.
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.2
Honig, B.3
-
67
-
-
0002309097
-
PLS - Partial least-squares projections to latent structures
-
Kubinyi, H., Ed.; ESCOM Science Publishers: Leiden
-
Wold, S.; Johansson, E.; Cocchi, C. PLS - Partial least-squares projections to latent structures. In 3D QSAR in Drug Design; Kubinyi, H., Ed.; ESCOM Science Publishers: Leiden, 1993; pp 523-550.
-
(1993)
3D QSAR in Drug Design
, pp. 523-550
-
-
Wold, S.1
Johansson, E.2
Cocchi, C.3
-
68
-
-
0028106321
-
Peptide binding to the most frequent HLA. A class I alleles measured by quantitative molecular binding assays
-
Sette, A.; Sidney, J.; Del Guercio, M. F.; Southwood, S.; Ruppert, J.; Dahlberg, J.; Grey, H. M.; Kubo, R. T. Peptide binding to the most frequent HLA. A class I alleles measured by quantitative molecular binding assays. Mol. Immunol. 1994, 31, 813-822.
-
(1994)
Mol. Immunol.
, vol.31
, pp. 813-822
-
-
Sette, A.1
Sidney, J.2
Del Guercio, M.F.3
Southwood, S.4
Ruppert, J.5
Dahlberg, J.6
Grey, H.M.7
Kubo, R.T.8
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