-
1
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin, I., B. Y. Ma, H. Wolfson, and R. Nussinov. 2002. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins. 47:409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.Y.2
Wolfson, H.3
Nussinov, R.4
-
2
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith, G. R., and M. J. E. Sternberg. 2002. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12: 28-35.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
3
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan, A. A., and K. S. Thorn. 1998. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1-9.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
-
4
-
-
0242696091
-
Free energy calculations and ligand binding
-
Brandsdal, B. O., F. Österberg, M. Almlöf, I. Feierberg, V. B. Luzhkov, and J. Åqvist. 2003. Free energy calculations and ligand binding. Adv. Protein Chem. 66:123-158.
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 123-158
-
-
Brandsdal, B.O.1
Österberg, F.2
Almlöf, M.3
Feierberg, I.4
Luzhkov, V.B.5
Åqvist, J.6
-
5
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman, P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
6
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Åqvist, J., C. Medina, and J. E. Samuelsson. 1994. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-391.
-
(1994)
Protein Eng.
, vol.7
, pp. 385-391
-
-
Åqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
8
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices
-
Srinivasan, J., T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120:9401-9409.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
9
-
-
0027087369
-
Calculation of the free-energy of association for protein complexes
-
Horton, N., and M. Lewis. 1992. Calculation of the free-energy of association for protein complexes. Protein Sci. 1:169-181.
-
(1992)
Protein Sci.
, vol.1
, pp. 169-181
-
-
Horton, N.1
Lewis, M.2
-
10
-
-
0033568644
-
Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
-
Massova, I., and P. A. Kollman. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-8143.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
11
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A., I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, and T. E. Cheatham. 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33:889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
12
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke, H., and D. A. Case. 2004. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25:238-250.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
13
-
-
0030134110
-
On the validity of electrostatic linear response in polar solvents
-
Åqvist, J., and T. Hansson. 1996. On the validity of electrostatic linear response in polar solvents. J. Phys. Chem. 100:9512-9521.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 9512-9521
-
-
Åqvist, J.1
Hansson, T.2
-
14
-
-
3042549928
-
Binding affinity prediction with different force fields: Examination of the linear interaction energy method
-
Almlöf, M., B. O. Brandsdal, and J. Åqvist. 2004. Binding affinity prediction with different force fields: examination of the linear interaction energy method. J. Comput. Chem. 25:1242-1254.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1242-1254
-
-
Almlöf, M.1
Brandsdal, B.O.2
Åqvist, J.3
-
15
-
-
0026596911
-
Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
-
Lee, F. S., Z. T. Chu, M. B. Bolger, and A. Warshel. 1992. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5:215-228.
-
(1992)
Protein Eng.
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.T.2
Bolger, M.B.3
Warshel, A.4
-
16
-
-
0034925093
-
Computational analysis of binding of P1 variants to trypsin
-
Brandsdal, B. O., J. Åqvist, and A. O. Smalås. 2001. Computational analysis of binding of P1 variants to trypsin. Protein Sci. 10:1584-1595.
-
(2001)
Protein Sci.
, vol.10
, pp. 1584-1595
-
-
Brandsdal, B.O.1
Åqvist, J.2
Smalås, A.O.3
-
17
-
-
0033612211
-
Interscaffolding additivity: Binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases
-
Krowarsch, D., M. Dadlez, O. Buczek, I. Krokoszynska, A. O. Smalås, and J. Otlewski. 1999. Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases. J. Mol. Biol. 289:175-186.
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 175-186
-
-
Krowarsch, D.1
Dadlez, M.2
Buczek, O.3
Krokoszynska, I.4
Smalås, A.O.5
Otlewski, J.6
-
18
-
-
0032232405
-
Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
-
Marelius, J., K. Kolmodin, I. Feierberg, and J. Åqvist. 1998. Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graph. Model. 16:213-225, 261.
-
(1998)
J. Mol. Graph. Model.
, vol.16
-
-
Marelius, J.1
Kolmodin, K.2
Feierberg, I.3
Åqvist, J.4
-
19
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
20
-
-
0032923399
-
High-resolution structures of three new trypsin-squash-inhibitor complexes: A detailed comparison with other trypsins and their complexes
-
Helland, R., G. I. Berglund, J. Otlewski, W. Apostoluk, O. A. Andersen, N. P. Willassen, and A. O. Smalås. 1999. High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes. Acta Crystallogr. D. 55:139-148.
-
(1999)
Acta Crystallogr. D
, vol.55
, pp. 139-148
-
-
Helland, R.1
Berglund, G.I.2
Otlewski, J.3
Apostoluk, W.4
Andersen, O.A.5
Willassen, N.P.6
Smalås, A.O.7
-
21
-
-
84889120137
-
Improved methods for building protein models in electron-density maps and the location of errors in these models
-
Jones, T. A., J. Y. Zou, S. W. Cowan, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr. A. 47:110-119.
-
(1991)
Acta Crystallogr. A
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
22
-
-
0022801412
-
X-ray crystal-structure of the complex of human-leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor
-
Bode, W., A. Z. Wei, R. Huber, E. Meyer, J. Travis, and S. Neumann. 1986. X-ray crystal-structure of the complex of human-leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J. 5:2453-2458.
-
(1986)
EMBO J.
, vol.5
, pp. 2453-2458
-
-
Bode, W.1
Wei, A.Z.2
Huber, R.3
Meyer, E.4
Travis, J.5
Neumann, S.6
-
23
-
-
0023198896
-
Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution
-
Fujinaga, M., A. R. Sielecki, R. J. Read, W. Ardelt, M. Laskowski, Jr., and M. N. James. 1987. Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195:397-418.
-
(1987)
J. Mol. Biol.
, vol.195
, pp. 397-418
-
-
Fujinaga, M.1
Sielecki, A.R.2
Read, R.J.3
Ardelt, W.4
Laskowski Jr., M.5
James, M.N.6
-
24
-
-
0000115003
-
A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
-
Lee, F. S., and A. Warshel. 1992. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97:3100-3107.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 3100-3107
-
-
Lee, F.S.1
Warshel, A.2
-
25
-
-
0004016501
-
Comparison of simple potential function for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential function for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
26
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
27
-
-
0035875953
-
Electrostatic effects play a central role in cold adaptation of trypsin
-
Brandsdal, B. O., A. O. Smalås, and J. Åqvist. 2001. Electrostatic effects play a central role in cold adaptation of trypsin. FEBS Lett. 499:171-175.
-
(2001)
FEBS Lett.
, vol.499
, pp. 171-175
-
-
Brandsdal, B.O.1
Smalås, A.O.2
Åqvist, J.3
-
28
-
-
0001205818
-
Electrostatic effects in water-accessible regions of proteins
-
Mehler, E. I., and G. Eichele. 1984. Electrostatic effects in water-accessible regions of proteins. Biochemistry. 23:3887-3891.
-
(1984)
Biochemistry
, vol.23
, pp. 3887-3891
-
-
Mehler, E.I.1
Eichele, G.2
-
29
-
-
0028856716
-
Water molecules participate in proteinase-inhibitor interactions: Crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B
-
Huang, K., W. Lu, S. Anderson, M. Laskowski, Jr., and M. N. James. 1995. Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B. Protein Sci. 4:1985-1997.
-
(1995)
Protein Sci.
, vol.4
, pp. 1985-1997
-
-
Huang, K.1
Lu, W.2
Anderson, S.3
Laskowski Jr., M.4
James, M.N.5
-
30
-
-
0041620630
-
C-2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: Synthesis and theoretical predictions
-
Ersmark, K., I. Feierberg, S. Bjelic, J. Hulten, B. Samuelsson, J. Åqvist, and A. Hallberg. 2003. C-2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: Synthesis and theoretical predictions. Bioorg. Med. Chem. 11:3723-3733.
-
(2003)
Bioorg. Med. Chem.
, vol.11
, pp. 3723-3733
-
-
Ersmark, K.1
Feierberg, I.2
Bjelic, S.3
Hulten, J.4
Samuelsson, B.5
Åqvist, J.6
Hallberg, A.7
-
31
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
Hansson, T., J. Marelius, and J. Åqvist. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comput. Aided Mol. Des. 12:27-35.
-
(1998)
J. Comput. Aided Mol. Des.
, vol.12
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Åqvist, J.3
-
32
-
-
0032014129
-
Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
-
Marelius, J., M. Graffner-Nordberg, T. Hansson, A. Hallberg, and J. Åqvist. 1998. Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. Comput. Aided Mol. Des. 12:119-131.
-
(1998)
J. Comput. Aided Mol. Des.
, vol.12
, pp. 119-131
-
-
Marelius, J.1
Graffner-Nordberg, M.2
Hansson, T.3
Hallberg, A.4
Åqvist, J.5
-
33
-
-
9144243695
-
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity
-
Ersmark, K., I. Feierberg, S. Bjelic, E. Hamelink, F. Hackett, M. J. Blackman, J. Hulten, B. Samuelsson, J. Åqvist, and A. Hallberg. 2004. Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity. J. Med. Chem. 47:110-122.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 110-122
-
-
Ersmark, K.1
Feierberg, I.2
Bjelic, S.3
Hamelink, E.4
Hackett, F.5
Blackman, M.J.6
Hulten, J.7
Samuelsson, B.8
Åqvist, J.9
Hallberg, A.10
-
34
-
-
0035913056
-
Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii
-
Graffner-Nordberg, M., K. Kolmodin, J. Åqvist, S. F. Queener, and A. Hallberg. 2001. Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. J. Med. Chem. 44:2391-2402.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 2391-2402
-
-
Graffner-Nordberg, M.1
Kolmodin, K.2
Åqvist, J.3
Queener, S.F.4
Hallberg, A.5
-
35
-
-
1842611389
-
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements
-
Leiros, H. K. S., B. O. Brandsdal, O. A. Andersen, V. Os, I. Leiros, R. Helland, J. Otlewski, N. P. Willassen, and A. O. Smalås. 2004. Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements. Protein Sci. 13:1056-1070.
-
(2004)
Protein Sci.
, vol.13
, pp. 1056-1070
-
-
Leiros, H.K.S.1
Brandsdal, B.O.2
Andersen, O.A.3
Os, V.4
Leiros, I.5
Helland, R.6
Otlewski, J.7
Willassen, N.P.8
Smalås, A.O.9
-
36
-
-
0035957732
-
Mechanisms of tetraethylammonium ion block in the KcsA potassium channel
-
Luzhkov, V. B., and J. Åqvist. 2001. Mechanisms of tetraethylammonium ion block in the KcsA potassium channel. FEBS Lett. 495:191-196.
-
(2001)
FEBS Lett.
, vol.495
, pp. 191-196
-
-
Luzhkov, V.B.1
Åqvist, J.2
-
37
-
-
0034257240
-
Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site
-
Gorfe, A. A., B. O. Brandsdal, H. K. Leiros, R. Helland, and A. O. Smalås. 2000. Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: qualitative evaluation of electrostatic differences at the substrate binding site. Proteins. 40:207-217.
-
(2000)
Proteins
, vol.40
, pp. 207-217
-
-
Gorfe, A.A.1
Brandsdal, B.O.2
Leiros, H.K.3
Helland, R.4
Smalås, A.O.5
-
38
-
-
0031581824
-
Binding of amino acid side-chains to S1 cavities of serine proteinases
-
Lu, W., I. Apostol, M. A. Qasim, N. Warne, R. Wynn, W. L. Zhang, S. Anderson, Y. W. Chiang, E. Ogin, I. Rothberg, K. Ryan, and M. Laskowski, Jr. 1997. Binding of amino acid side-chains to S1 cavities of serine proteinases. J. Mol. Biol. 266:441-461.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 441-461
-
-
Lu, W.1
Apostol, I.2
Qasim, M.A.3
Warne, N.4
Wynn, R.5
Zhang, W.L.6
Anderson, S.7
Chiang, Y.W.8
Ogin, E.9
Rothberg, I.10
Ryan, K.11
Laskowski Jr., M.12
-
39
-
-
0028916599
-
A hot-spot of binding-energy in a hormone-receptor interface
-
Clackson, T., and J. A. Wells. 1995. A hot-spot of binding-energy in a hormone-receptor interface. Science. 267:383-386.
-
(1995)
Science
, vol.267
, pp. 383-386
-
-
Clackson, T.1
Wells, J.A.2
-
40
-
-
0028810673
-
Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation
-
Qasim, M. A., M. R. Ranjbar, R. Wynn, S. Anderson, and M. J. Laskowski. 1995. Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation. J. Biol. Chem. 270: 27419-27422.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 27419-27422
-
-
Qasim, M.A.1
Ranjbar, M.R.2
Wynn, R.3
Anderson, S.4
Laskowski, M.J.5
-
41
-
-
0342321950
-
Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
-
Sham, Y. Y., Z. T. Chu, H. Tao, and A. Warshel. 2000. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins. 39:393-407.
-
(2000)
Proteins
, vol.39
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
|