-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, 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
-
3
-
-
0004195760
-
-
University of California, San Francisco
-
Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham 3rd, J. M. Wang, W. S. Ross, C. Simmerling, T. Darden, K. M. Merz, R. V. Stanton, A. Cheng, J. J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman. 2002. AMBER 7. University of California, San Francisco.
-
(2002)
AMBER 7
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.M.5
Ross, W.S.6
Simmerling, C.7
Darden, T.8
Merz, K.M.9
Stanton, R.V.10
Cheng, A.11
Vincent, J.J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.L.20
Singh, U.C.21
Weiner, P.22
Kollman, P.A.23
more..
-
4
-
-
0038526303
-
ZDOCK: An initial-stage protein-docking algorithm
-
Chen, R., L. Li, and Z. P. Weng. 2003a. ZDOCK: An initial-stage protein-docking algorithm. Proteins. 52:80-87.
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.P.3
-
5
-
-
0037561868
-
ZDOCK predictions for the CAPRI Challenge
-
Chen, R., W. W. Tong, J. Mintseris, L. Li, and Z. P. Weng. 2003b. ZDOCK predictions for the CAPRI Challenge. Proteins. 52:68-73.
-
(2003)
Proteins
, vol.52
, pp. 68-73
-
-
Chen, R.1
Tong, W.W.2
Mintseris, J.3
Li, L.4
Weng, Z.P.5
-
6
-
-
0035066437
-
Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel
-
Cui, M., J. H. Shen, J. M. Briggs, X. M. Luo, X. J. Tan, H. L. Jiang, K. X. Chen, and R. Y. Ji. 2001. Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel. Biophys. J. 80:1659-1669.
-
(2001)
Biophys. J.
, vol.80
, pp. 1659-1669
-
-
Cui, M.1
Shen, J.H.2
Briggs, J.M.3
Luo, X.M.4
Tan, X.J.5
Jiang, H.L.6
Chen, K.X.7
Ji, R.Y.8
-
7
-
-
0036302289
-
Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the small-conductance calcium-activated potassium channels
-
Cui, M., J. H. Shen, J. M. Briggs, W. Fu, J. J. Wu, Y. M. Zhang, X. M. Luo, Z. W. Qi, R. Y. Ji, H. L. Jiang, and K. X. Chen. 2002. Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the small-conductance calcium-activated potassium channels. J. Mol. Biol. 318:417-428.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 417-428
-
-
Cui, M.1
Shen, J.H.2
Briggs, J.M.3
Fu, W.4
Wu, J.J.5
Zhang, Y.M.6
Luo, X.M.7
Qi, Z.W.8
Ji, R.Y.9
Jiang, H.L.10
Chen, K.X.11
-
8
-
-
0032973257
-
Three-dimensional structure of scorpion toxins: Towards a new model of interaction with potassium channels
-
Darbon, H., E. Blanc, and J. M. Sabatier. 1999. Three-dimensional structure of scorpion toxins: towards a new model of interaction with potassium channels. Perspect. Drug Discov. 15/16:41-60.
-
(1999)
Perspect. Drug Discov.
, vol.15-16
, pp. 41-60
-
-
Darbon, H.1
Blanc, E.2
Sabatier, J.M.3
-
9
-
-
0034704075
-
+ channels in human leukemic Jurkat T cells. Molecular cloning, biochemical and functional characterization
-
+ channels in human leukemic Jurkat T cells. Molecular cloning, biochemical and functional characterization. J. Biol. Chem. 275:39954-39963.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 39954-39963
-
-
Desai, R.1
Peretz, A.2
Idelson, H.3
Lazarovici, P.4
Attali, B.5
-
10
-
-
0032478818
-
+ conduction and selectivity
-
+ conduction and selectivity. Science. 280:69-77.
-
(1998)
Science
, vol.280
, pp. 69-77
-
-
Doyle, D.A.1
Cabral, J.M.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Chait, B.T.7
MacKinnon, R.8
-
11
-
-
0036840108
-
+ channel: A computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles
-
+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles. Biophys. J. 83:2595-2609.
-
(2002)
Biophys. J.
, vol.83
, pp. 2595-2609
-
-
Eriksson, M.A.L.1
Roux, B.2
-
12
-
-
0036841675
-
Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels
-
Fu, W., M. Cui, J. M. Briggs, X. Q. Huang, B. Xiong, Y. M. Zhang, X. M. Luo, J. H. Shen, R. Y. Ji, H. L. Jiang, and K. X. Chen. 2002. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels. Biophys. J. 83:2370-2385.
-
(2002)
Biophys. J.
, vol.83
, pp. 2370-2385
-
-
Fu, W.1
Cui, M.2
Briggs, J.M.3
Huang, X.Q.4
Xiong, B.5
Zhang, Y.M.6
Luo, X.M.7
Shen, J.H.8
Ji, R.Y.9
Jiang, H.L.10
Chen, K.X.11
-
14
-
-
0028276482
-
+ channel: Peptide and channel residues mediating molecular recognition
-
+ channel: peptide and channel residues mediating molecular recognition. Neuron. 12:1377-1388.
-
(1994)
Neuron
, vol.12
, pp. 1377-1388
-
-
Goldstein, S.A.1
Pheasant, D.J.2
Miller, C.3
-
15
-
-
0042266913
-
A conserved domain in axonal targeting of Kv1 (Shaker) voltage-gated potassium channels
-
Gu, C., and Y. N. Jan. 2003. A conserved domain in axonal targeting of Kv1 (Shaker) voltage-gated potassium channels. Science. 301:646-649.
-
(2003)
Science
, vol.301
, pp. 646-649
-
-
Gu, C.1
Jan, Y.N.2
-
16
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex, N., and M. C. Peitsch. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18:2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
17
-
-
0034716751
-
A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning
-
Kuhn, B., and P. A. Kollman. 2000. A ligand that is predicted to bind better to avidin than biotin: insights from computational fluorine scanning. J. Am. Chem. Soc. 122:3909-3916.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 3909-3916
-
-
Kuhn, B.1
Kollman, P.A.2
-
18
-
-
0026013375
-
Binding and toxicity of apamin. Characterization of the active site
-
Labbe-Jullie, C., C. Granier, F. Albericio, M. L. Defendini, B. Ceard, H. Rochat, and J. Van Rietschoten. 1991. Binding and toxicity of apamin. Characterization of the active site. Eur. J. Biochem. 196:639-645.
-
(1991)
Eur. J. Biochem.
, vol.196
, pp. 639-645
-
-
Labbe-Jullie, C.1
Granier, C.2
Albericio, F.3
Defendini, M.L.4
Ceard, B.5
Rochat, H.6
Van Rietschoten, J.7
-
19
-
-
0032478696
-
Structural conservation in prokaryotic and eukaryotic potassium channels
-
Mackinnon, R., S. L. Cohen, A. Kuo, A. Lee, and B. T. Chait. 1998. Structural conservation in prokaryotic and eukaryotic potassium channels. Science. 280:106-109.
-
(1998)
Science
, vol.280
, pp. 106-109
-
-
Mackinnon, R.1
Cohen, S.L.2
Kuo, A.3
Lee, A.4
Chait, B.T.5
-
20
-
-
0028811207
-
Determination of the three-dimensional solution structure of scyllatoxin by IH nuclear magnetic resonance
-
Martins, J. C., F. J. M. Van de Ven, and F. A. M. Borremans. 1995. Determination of the three-dimensional solution structure of scyllatoxin by IH nuclear magnetic resonance. J. Mol. Biol. 253:590-603.
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 590-603
-
-
Martins, J.C.1
Van De Ven, F.J.M.2
Borremans, F.A.M.3
-
21
-
-
0042710087
-
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
-
22
-
-
0026666693
-
Mapping function to structure in a channel-blocking peptide: Electrostatic mutants of charybdotoxin
-
Park, C. S., and C. Miller. 1992. Mapping function to structure in a channel-blocking peptide: electrostatic mutants of charybdotoxin. Biochemistry. 31:7749-7755.
-
(1992)
Biochemistry
, vol.31
, pp. 7749-7755
-
-
Park, C.S.1
Miller, C.2
-
23
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation approximate Bom radii
-
Qiu, D., P. S. Shehkin, F. P. Hollinger, and W. C. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation approximate Bom radii. J. Phys. Chem. 101:3005-3014.
-
(1997)
J. Phys. Chem.
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shehkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
25
-
-
0027480617
-
+ channels with increased affinity
-
+ channels with increased affinity. Biochemistry, 32:2763-2770.
-
(1993)
Biochemistry
, vol.32
, pp. 2763-2770
-
-
Sabatier, J.M.1
Zerrouk, H.2
Darbon, H.3
Mabrouk, K.4
Benslimane, A.5
Rochat, H.6
Martin-Eauclaire, M.F.7
Van Rietschoten, J.8
-
26
-
-
0035900701
-
+ channel, SkCa2
-
+ channel, SkCa2. J. Biol. Chem. 276:43145-43151.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 43145-43151
-
-
Shakkottai, V.G.1
Regaya, I.2
Wulff, H.3
Fajloun, Z.4
Tomita, H.5
Fathallah, M.6
Cahalan, M.D.7
Gargus, J.J.8
Sabatier, J.M.9
Chandy, K.G.10
-
27
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith, G. R., and M. J. E. Stemberg. 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
Stemberg, M.J.E.2
-
28
-
-
0036027943
-
SCORPION, a molecular database of scorpion toxins
-
Srinivasan, K. N., P. Gopalakrishnakone, P. T. Tan, K. C. Chew, B. Cheng, R. M. Kini, J. L. Y. Koh, S. H. Seah, and V. Brusic. 2002. SCORPION, a molecular database of scorpion toxins. Toxicon. 40:23-31.
-
(2002)
Toxicon
, vol.40
, pp. 23-31
-
-
Srinivasan, K.N.1
Gopalakrishnakone, P.2
Tan, P.T.3
Chew, K.C.4
Cheng, B.5
Kini, R.M.6
Koh, J.L.Y.7
Seah, S.H.8
Brusic, V.9
-
29
-
-
14244273182
-
Theory and application of the generalized Born solvation model in macromolecular simulations
-
Tsui, V., and D. A. Case. 2001. Theory and application of the generalized Born solvation model in macromolecular simulations. Biopolymers. 56:275-291.
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
31
-
-
13044292627
-
Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein
-
Vita, C., E. Drakopoulou, J. Vizzavona, S. Rochette, L. Martin, A. Menez, C. Roumestand, Y. S. Yang, L. Ylisastigui, A. Benjouad, and J. G. Gluckman. 1999. Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein. Proc. Natl. Acad. Sci. USA. 96:13091-13096.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 13091-13096
-
-
Vita, C.1
Drakopoulou, E.2
Vizzavona, J.3
Rochette, S.4
Martin, L.5
Menez, A.6
Roumestand, C.7
Yang, Y.S.8
Ylisastigui, L.9
Benjouad, A.10
Gluckman, J.G.11
-
32
-
-
0001398008
-
How well does a RESP (restrained electrostatic potential) model do in calculating the conformational energies of organic and biological molecules?
-
Wang, J., P. Cieplak, and P. A. Kollman. 2000. How well does a RESP (restrained electrostatic potential) model do in calculating the conformational energies of organic and biological molecules? J. Comput. Chem. 21:1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
33
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
Wang, J. M., P. Morin, W. Wang, and P. K. Kollman. 2001. Use of MM-PBSA in reproducing the binding free energies to HIV-1 of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 123:5221-5230.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5221-5230
-
-
Wang, J.M.1
Morin, P.2
Wang, W.3
Kollman, P.K.4
|