-
1
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland D. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958;44:98-104.
-
(1958)
Proc Natl Acad Sci USA
, vol.44
, pp. 98-104
-
-
Koshland, D.1
-
3
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai CJ, Kumar S, Ma BY, Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci 1999;8:1181-1190.
-
(1999)
Protein Sci
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.Y.3
Nussinov, R.4
-
4
-
-
0035451185
-
Structured disorder and conformational selection
-
Tsai CJ, Ma BY, Sham YY, Kumar S, Nussinov R. Structured disorder and conformational selection. Proteins: Struct Funct Genet 2001;44:418-427.
-
(2001)
Proteins: Struct Funct Genet
, vol.44
, pp. 418-427
-
-
Tsai, C.J.1
Ma, B.Y.2
Sham, Y.Y.3
Kumar, S.4
Nussinov, R.5
-
5
-
-
0031746754
-
Statistical thermodynamic linkage between conformational and binding equilibria
-
Freire E. Statistical thermodynamic linkage between conformational and binding equilibria. Adv Protein Chem 1998;51:255-279.
-
(1998)
Adv Protein Chem
, vol.51
, pp. 255-279
-
-
Freire, E.1
-
6
-
-
0027943261
-
Conformational isomerism and the diversity of antibodies
-
Foote J, Milstein C. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 1994;91:10370-10374.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 10370-10374
-
-
Foote, J.1
Milstein, C.2
-
7
-
-
24644521419
-
Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition
-
James LC, Tawfik DS. Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proc Natl Acad Sci USA 2005;102:12730-12735.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 12730-12735
-
-
James, L.C.1
Tawfik, D.S.2
-
8
-
-
0032966864
-
Antigen recognition by conformational selection
-
Berger C, Weber-Bornhauser S, Eggenberger J, Hanes J, Pluckthun A, Bosshard H. Antigen recognition by conformational selection. FEBS Lett 1999;450:149-153.
-
(1999)
FEBS Lett
, vol.450
, pp. 149-153
-
-
Berger, C.1
Weber-Bornhauser, S.2
Eggenberger, J.3
Hanes, J.4
Pluckthun, A.5
Bosshard, H.6
-
9
-
-
0344441463
-
Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: Evidence of conformational heterogeneity
-
Aparicio R, Ferreira ST, Polikarpov I. Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity. J Mol Biol 2003;334:1023-1041.
-
(2003)
J Mol Biol
, vol.334
, pp. 1023-1041
-
-
Aparicio, R.1
Ferreira, S.T.2
Polikarpov, I.3
-
10
-
-
0029000872
-
Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand-gated
-
Williams JC, Mcdermott AE. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand-gated. Biochemistry 1995;34:8309-8319.
-
(1995)
Biochemistry
, vol.34
, pp. 8309-8319
-
-
Williams, J.C.1
Mcdermott, A.E.2
-
11
-
-
0031941134
-
Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus
-
Alvarez M, Zeelen J, Mainfroid V, Rentier-Delrue F, Martial J, Wyns L, Wierenga R, Maes D. Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. J Biol Chem 1998;273:2199-2206.
-
(1998)
J Biol Chem
, vol.273
, pp. 2199-2206
-
-
Alvarez, M.1
Zeelen, J.2
Mainfroid, V.3
Rentier-Delrue, F.4
Martial, J.5
Wyns, L.6
Wierenga, R.7
Maes, D.8
-
12
-
-
0028298146
-
Crystal structure of recombinant human triosephosphate isomerase at 2.8 Å resolution. Triosephophate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme
-
Mande S, Mainfroid V, Kalk K, Martial J, Hol W. Crystal structure of recombinant human triosephosphate isomerase at 2.8 Å resolution. Triosephophate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme. Proteins 1994;3:810-821.
-
(1994)
Proteins
, vol.3
, pp. 810-821
-
-
Mande, S.1
Mainfroid, V.2
Kalk, K.3
Martial, J.4
Hol, W.5
-
13
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2003;2:527-541.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
14
-
-
0042853244
-
Protein flexibility and computer-aided drug design
-
Wong CF, McCammon JA. Protein flexibility and computer-aided drug design. Annu Rev Pharmacol Toxicol 2003;43:31-45.
-
(2003)
Annu Rev Pharmacol Toxicol
, vol.43
, pp. 31-45
-
-
Wong, C.F.1
McCammon, J.A.2
-
15
-
-
0036680063
-
Protein flexibility and drug design: How to hit a moving target
-
Carlson HA. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol 2002;6:447-452.
-
(2002)
Curr Opin Chem Biol
, vol.6
, pp. 447-452
-
-
Carlson, H.A.1
-
16
-
-
0041989635
-
Conformational flexibility models for the receptor in structure based drug design
-
Teodoro M, Kavraki L. Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 2003;9:1635-1648.
-
(2003)
Curr Pharm Des
, vol.9
, pp. 1635-1648
-
-
Teodoro, M.1
Kavraki, L.2
-
17
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001;308:377-395.
-
(2001)
J Mol Biol
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
18
-
-
0031302358
-
Flexible protein-ligand docking by global energy optimization in internal coordinates
-
Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997; (Suppl 1):215-220.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 215-220
-
-
Totrov, M.1
Abagyan, R.2
-
19
-
-
0042282803
-
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
-
Taylor R, Jewsbury P, Essex J. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J Comput Chem 2003;24:1637-1656.
-
(2003)
J Comput Chem
, vol.24
, pp. 1637-1656
-
-
Taylor, R.1
Jewsbury, P.2
Essex, J.3
-
20
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49:534-553.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
21
-
-
0346167517
-
Technique for developing a pharmacophore model that accommodates inherent protein flexibility: An application to HIV-1 integrase
-
Guner OF, editor, La Jolla, CA: International University Line;
-
Masukawa KM, Carlson HA, McCammon JA. Technique for developing a pharmacophore model that accommodates inherent protein flexibility: an application to HIV-1 integrase. In: Guner OF, editor. Pharmacophore perception, development and use in drug design. La Jolla, CA: International University Line; 2000. p 537.
-
(2000)
Pharmacophore perception, development and use in drug design
, pp. 537
-
-
Masukawa, K.M.1
Carlson, H.A.2
McCammon, J.A.3
-
22
-
-
0037231646
-
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
-
Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003;68:47-62.
-
(2003)
Biopolymers
, vol.68
, pp. 47-62
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
23
-
-
33745880692
-
Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase
-
Frembgen-Kesner T, Elcock A. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. J Mol Biol 2006;359:202-214.
-
(2006)
J Mol Biol
, vol.359
, pp. 202-214
-
-
Frembgen-Kesner, T.1
Elcock, A.2
-
24
-
-
28644443463
-
Molecular docking of balanol to dynamics snapshots of protein kinase A
-
Wong CF, Kua J, Zhang Y, Straatsma TP, McCammon JA. Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins 2005;61:850-858.
-
(2005)
Proteins
, vol.61
, pp. 850-858
-
-
Wong, C.F.1
Kua, J.2
Zhang, Y.3
Straatsma, T.P.4
McCammon, J.A.5
-
25
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
Alonso A, Bliznyuk A, Gready J. Combining docking and molecular dynamic simulations in drug design. Med Res Rev 2006;26:531-568.
-
(2006)
Med Res Rev
, vol.26
, pp. 531-568
-
-
Alonso, A.1
Bliznyuk, A.2
Gready, J.3
-
26
-
-
18144418170
-
Protein structural change upon ligand binding: Linear response theory
-
Ikeguchi M, Ueno J, Sato M, Kidera A. Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 2005;94:078102.
-
(2005)
Phys Rev Lett
, vol.94
, pp. 078102
-
-
Ikeguchi, M.1
Ueno, J.2
Sato, M.3
Kidera, A.4
-
27
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005;127:9632-9640.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
28
-
-
0031892160
-
Protein conformer selection by ligand binding observed with crystallography
-
Cao Y, Musah RA, Wilcox SK, Goodin DB, McRee DE. Protein conformer selection by ligand binding observed with crystallography. Protein Sci 1998;7:72-78.
-
(1998)
Protein Sci
, vol.7
, pp. 72-78
-
-
Cao, Y.1
Musah, R.A.2
Wilcox, S.K.3
Goodin, D.B.4
McRee, D.E.5
-
29
-
-
0031043155
-
Rapid loop dynamics of Yersinia protein tyrosine phosphatases
-
Juszczak LJ, Zhang ZY, Wu L, Gottfried DS, Eads DD. Rapid loop dynamics of Yersinia protein tyrosine phosphatases. Biochemistry 1997;36:2227-2236.
-
(1997)
Biochemistry
, vol.36
, pp. 2227-2236
-
-
Juszczak, L.J.1
Zhang, Z.Y.2
Wu, L.3
Gottfried, D.S.4
Eads, D.D.5
-
30
-
-
6344245774
-
Incorporating protein flexibility in structure-based drug discovery: Using HIV-1 protease as a test case
-
Meagher KL, Carlson HA. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J Am Chem Soc 2004;126:13276-13281.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 13276-13281
-
-
Meagher, K.L.1
Carlson, H.A.2
-
31
-
-
0029651191
-
Functionally diverse enzyme superfamily that abstracts the α-protons of carboxylic-acids
-
Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA. Functionally diverse enzyme superfamily that abstracts the α-protons of carboxylic-acids. Science 1995;267:1159-1161.
-
(1995)
Science
, vol.267
, pp. 1159-1161
-
-
Babbitt, P.C.1
Mrachko, G.T.2
Hasson, M.S.3
Huisman, G.W.4
Kolter, R.5
Ringe, D.6
Petsko, G.A.7
Kenyon, G.L.8
Gerlt, J.A.9
-
32
-
-
0035951075
-
Evolution of enzymatic activities in the enolase superfamily: Crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis
-
Gulick AM, Schmidt DMZ, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry 2001;40:15716-15724.
-
(2001)
Biochemistry
, vol.40
, pp. 15716-15724
-
-
Gulick, A.M.1
Schmidt, D.M.Z.2
Gerlt, J.A.3
Rayment, I.4
-
33
-
-
4043106218
-
Evolution of enzymatic activities in the enolase superfamily: Structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis
-
Klenchin VA, Schmidt DM, Gerlt JA, Rayment I. Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis. Biochemistry 2004;43:10370-10378.
-
(2004)
Biochemistry
, vol.43
, pp. 10370-10378
-
-
Klenchin, V.A.1
Schmidt, D.M.2
Gerlt, J.A.3
Rayment, I.4
-
34
-
-
0027964654
-
2+)-complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1 Å resolution
-
2+)-complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1 Å resolution. Biochemistry 1994;33:9333-9342.
-
(1994)
Biochemistry
, vol.33
, pp. 9333-9342
-
-
Wedekind, J.E.1
Poyner, R.R.2
Reed, G.H.3
Rayment, I.4
-
35
-
-
0034681940
-
Crystal structure at 2.4 Å resolution of Borrelia burgdorferi inosine 5′-monophosphate dehydrogenase: Evidence of a substrate-induced hinged-lid motion by loop 6
-
McMillan FM, Cahoon M, White A, Hedstrom L, Petsko GA, Ringe D. Crystal structure at 2.4 Å resolution of Borrelia burgdorferi inosine 5′-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6. Biochemistry 2000;39:4533-4542.
-
(2000)
Biochemistry
, vol.39
, pp. 4533-4542
-
-
McMillan, F.M.1
Cahoon, M.2
White, A.3
Hedstrom, L.4
Petsko, G.A.5
Ringe, D.6
-
36
-
-
0025777309
-
Analysis of protein loop closure. Two types of hinges produce one motion in lactate-dehydrogenase
-
Gerstein M, Chothia C. Analysis of protein loop closure. Two types of hinges produce one motion in lactate-dehydrogenase. J Mol Biol 1991;220:133-149.
-
(1991)
J Mol Biol
, vol.220
, pp. 133-149
-
-
Gerstein, M.1
Chothia, C.2
-
37
-
-
0001056843
-
Efficient Monte Carlo methods for cyclic peptides
-
Wu MG, Deem MW. Efficient Monte Carlo methods for cyclic peptides. Mol Phys 1999;97:559-580.
-
(1999)
Mol Phys
, vol.97
, pp. 559-580
-
-
Wu, M.G.1
Deem, M.W.2
-
38
-
-
0038047149
-
Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling
-
Taylor JC, Markham GD. Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling. Arch Biochem Biophys 2003;415:164-171.
-
(2003)
Arch Biochem Biophys
, vol.415
, pp. 164-171
-
-
Taylor, J.C.1
Markham, G.D.2
-
39
-
-
0034235377
-
The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis
-
Okoniewska M, Tanaka T, Yada RY. The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis. Biochem J 2000;349:169-177.
-
(2000)
Biochem J
, vol.349
, pp. 169-177
-
-
Okoniewska, M.1
Tanaka, T.2
Yada, R.Y.3
-
40
-
-
0037426326
-
Interdependence of backbone flexibility, residue conservation, and enzyme function: A case study on 1,4-galactosyltransferase-I
-
Gunasekaran K, Ma BY, Ramakrishnan B, Qasba PK, Nussinov R. Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on 1,4-galactosyltransferase-I. Biochemistry 2003;42:3674-3687.
-
(2003)
Biochemistry
, vol.42
, pp. 3674-3687
-
-
Gunasekaran, K.1
Ma, B.Y.2
Ramakrishnan, B.3
Qasba, P.K.4
Nussinov, R.5
-
41
-
-
22744454355
-
The apo and ternary complex structures of a chemotherapeutic target: Human glycinamide ribonucleotide transformylase
-
Dahms TES, Sainz G, Giroux EL, Caperelli CA, Smith JL. The apo and ternary complex structures of a chemotherapeutic target: human glycinamide ribonucleotide transformylase. Biochemistry 2005;44:9841-9850.
-
(2005)
Biochemistry
, vol.44
, pp. 9841-9850
-
-
Dahms, T.E.S.1
Sainz, G.2
Giroux, E.L.3
Caperelli, C.A.4
Smith, J.L.5
-
42
-
-
0030800147
-
Crystal structures of a mutant (β K87T) tryptophan synthase α(2)β(2) complex with ligands bound to the active sites of the α-and β-subunits reveal ligand-induced conformational changes
-
Rhee S, Parris KD, Hyde CC, Ahmed SA, Miles EW, Davies DR. Crystal structures of a mutant (β K87T) tryptophan synthase α(2)β(2) complex with ligands bound to the active sites of the α-and β-subunits reveal ligand-induced conformational changes. Biochemistry 1997;36:7664-7680.
-
(1997)
Biochemistry
, vol.36
, pp. 7664-7680
-
-
Rhee, S.1
Parris, K.D.2
Hyde, C.C.3
Ahmed, S.A.4
Miles, E.W.5
Davies, D.R.6
-
43
-
-
0031592468
-
The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate
-
Taylor TC, Andersson I. The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. J Mol Biol 1997;265:432-444.
-
(1997)
J Mol Biol
, vol.265
, pp. 432-444
-
-
Taylor, T.C.1
Andersson, I.2
-
44
-
-
0035415662
-
Protein tyrosine phosphatases: Prospects for therapeutics
-
Zhang ZY. Protein tyrosine phosphatases: prospects for therapeutics. Curr Opin Chem Biol 2001;5:416-423.
-
(2001)
Curr Opin Chem Biol
, vol.5
, pp. 416-423
-
-
Zhang, Z.Y.1
-
45
-
-
0038199726
-
PTP1B: From the sidelines to the front lines!
-
Tonks NK. PTP1B: from the sidelines to the front lines! FEBS Lett 2003;546:140-148.
-
(2003)
FEBS Lett
, vol.546
, pp. 140-148
-
-
Tonks, N.K.1
-
46
-
-
0032777686
-
A novel series of non-nucleoside inhibitors of inosine 5′-monophosphate dehydrogenase with immunosuppressive activity
-
Franklin TJ, Morris WP, Jacobs VN, Culbert EJ, Heys CA, Ward WHJ, Cook PN, Jung F, Ple P. A novel series of non-nucleoside inhibitors of inosine 5′-monophosphate dehydrogenase with immunosuppressive activity. Biochem Pharmacol 1999;58:867-876.
-
(1999)
Biochem Pharmacol
, vol.58
, pp. 867-876
-
-
Franklin, T.J.1
Morris, W.P.2
Jacobs, V.N.3
Culbert, E.J.4
Heys, C.A.5
Ward, W.H.J.6
Cook, P.N.7
Jung, F.8
Ple, P.9
-
47
-
-
0037204010
-
Novel mycophenolic adenine bis(phosphonate) analogues as potential differentiation agents against human leukemia
-
Pankiewicz KW, Lesiak-Watanabe KB, Watanabe KA, Patterson SE, Jayaram HN, Yalowitz JA, Miller MD, Seidman M, Majumdar A, Prehna G, Goldstein BM. Novel mycophenolic adenine bis(phosphonate) analogues as potential differentiation agents against human leukemia. J Med Chem 2002;45:703-712.
-
(2002)
J Med Chem
, vol.45
, pp. 703-712
-
-
Pankiewicz, K.W.1
Lesiak-Watanabe, K.B.2
Watanabe, K.A.3
Patterson, S.E.4
Jayaram, H.N.5
Yalowitz, J.A.6
Miller, M.D.7
Seidman, M.8
Majumdar, A.9
Prehna, G.10
Goldstein, B.M.11
-
48
-
-
20644442880
-
The spermidine synthase of the malaria parasite Plasmodium falciparum: Molecular and biochemical characterisation of the polyamine synthesis enzyme
-
Haider N, Eschbach ML, Dias SD, Gilberger TW, Walter RD, Luersen K. The spermidine synthase of the malaria parasite Plasmodium falciparum: molecular and biochemical characterisation of the polyamine synthesis enzyme. Mol Biochem Parasitol 2005;142:224-236.
-
(2005)
Mol Biochem Parasitol
, vol.142
, pp. 224-236
-
-
Haider, N.1
Eschbach, M.L.2
Dias, S.D.3
Gilberger, T.W.4
Walter, R.D.5
Luersen, K.6
-
49
-
-
0141798673
-
Polyamine metabolism and cancer
-
Thomas T, Thomas TJ. Polyamine metabolism and cancer. J Cell Mol Med 2003;7:113-126.
-
(2003)
J Cell Mol Med
, vol.7
, pp. 113-126
-
-
Thomas, T.1
Thomas, T.J.2
-
50
-
-
13544275571
-
Virtual screening against highly charged active sites: Identifying substrates of αβ barrel enzymes
-
Kalyanaraman C, Bernacki K, Jacobson MP. Virtual screening against highly charged active sites: identifying substrates of αβ barrel enzymes. Biochemistry 2005;44:2059-2071.
-
(2005)
Biochemistry
, vol.44
, pp. 2059-2071
-
-
Kalyanaraman, C.1
Bernacki, K.2
Jacobson, M.P.3
-
51
-
-
0024394730
-
Biochemically directed therapy of leukemia with tiazofurin, a selective blocker of inosine 5′-phosphate dehydrogenase-activity
-
Tricot GJ, Jayaram HN, Lapis E, Natsumeda Y, Nichols CR, Kneebone P, Heerema N, Weber G, Hoffman R. Biochemically directed therapy of leukemia with tiazofurin, a selective blocker of inosine 5′-phosphate dehydrogenase-activity. Cancer Res 1989;49:3696-3701.
-
(1989)
Cancer Res
, vol.49
, pp. 3696-3701
-
-
Tricot, G.J.1
Jayaram, H.N.2
Lapis, E.3
Natsumeda, Y.4
Nichols, C.R.5
Kneebone, P.6
Heerema, N.7
Weber, G.8
Hoffman, R.9
-
52
-
-
27644450220
-
Conformational sampling of protein flexibility in generalized coordinates: Application to ligand docking
-
Kovacs JA, Cavasotto CN, Abagyan R. Conformational sampling of protein flexibility in generalized coordinates: application to ligand docking. J Comput Theor Nanosci 2005;2:354-361.
-
(2005)
J Comput Theor Nanosci
, vol.2
, pp. 354-361
-
-
Kovacs, J.A.1
Cavasotto, C.N.2
Abagyan, R.3
-
53
-
-
0032147007
-
Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
-
Sandak B, Wolfson HJ, Nussinov R. Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers. Proteins: Struct Funct Genet 1998;32:159-174.
-
(1998)
Proteins: Struct Funct Genet
, vol.32
, pp. 159-174
-
-
Sandak, B.1
Wolfson, H.J.2
Nussinov, R.3
-
54
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
55
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 2001;60:96-123.
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
56
-
-
0028122711
-
Crystal structure of Yersinia protein tyrosin phosphatase at 2.5 Å and the complex with tungstate
-
Stuckey J, Schubert H, Fauman E, Zhang Z, Dixon J, Saper M. Crystal structure of Yersinia protein tyrosin phosphatase at 2.5 Å and the complex with tungstate. Nature 1994;370:571-575.
-
(1994)
Nature
, vol.370
, pp. 571-575
-
-
Stuckey, J.1
Schubert, H.2
Fauman, E.3
Zhang, Z.4
Dixon, J.5
Saper, M.6
-
57
-
-
0026668340
-
Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase
-
Almassy R, Janson C, Kan C, Hostomska Z. Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase. Proc Natl Acad Sci USA 1992;89:6114-6118.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 6114-6118
-
-
Almassy, R.1
Janson, C.2
Kan, C.3
Hostomska, Z.4
-
58
-
-
21144451823
-
Control of spermidine and spermine levels in rat tissues by trans-4-methylcyclohexylamine, a spermidine-synthase inhibitor
-
Kobayashi M, Watanabe T, Xu YJ, Tatemori M, Goda H, Niitsu M, Shirahata A, Samejima K. Control of spermidine and spermine levels in rat tissues by trans-4-methylcyclohexylamine, a spermidine-synthase inhibitor. Biol Pharm Bull 2005;28:569-573.
-
(2005)
Biol Pharm Bull
, vol.28
, pp. 569-573
-
-
Kobayashi, M.1
Watanabe, T.2
Xu, Y.J.3
Tatemori, M.4
Goda, H.5
Niitsu, M.6
Shirahata, A.7
Samejima, K.8
-
59
-
-
0036142291
-
The crystal structure of spermidine synthase wih a multisubstrate adduct inhibitor
-
Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg A, Savchenko A. The crystal structure of spermidine synthase wih a multisubstrate adduct inhibitor. Nat Struct Biol 2002;9:27-31.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 27-31
-
-
Korolev, S.1
Ikeguchi, Y.2
Skarina, T.3
Beasley, S.4
Arrowsmith, C.5
Edwards, A.6
Joachimiak, A.7
Pegg, A.8
Savchenko, A.9
-
60
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;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
-
62
-
-
40549135412
-
-
Case DA, Darden TA, Cheatham TE, III, Simmerling LL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Hornak J, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA. AMBER 8; University of California, San Francisco, CA, 2004.
-
Case DA, Darden TA, Cheatham TE, III, Simmerling LL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Hornak J, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA. AMBER 8; University of California, San Francisco, CA, 2004.
-
-
-
-
63
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002;124:11258-11259.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
64
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Struct Funct Bioinf 2004;55:383-394.
-
(2004)
Proteins: Struct Funct Bioinf
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
65
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR. Molecular-dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
66
-
-
84952104504
-
An analysis of the accuracy of langevin and molecular-dynamics algorithms
-
Pastor RW, Brooks BR, Szabo A. An analysis of the accuracy of langevin and molecular-dynamics algorithms. Mol Phys 1988;65:1409-1419.
-
(1988)
Mol Phys
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
67
-
-
0026869597
-
Langevin dynamics of peptides - the frictional dependence of isomerization rates of N-acetylalanyl- N′-methylamide
-
Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides - the frictional dependence of isomerization rates of N-acetylalanyl- N′-methylamide. Biopolymers 1992;32:523-535.
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
68
-
-
36449009053
-
Molecular-dynamics algorithm for multiple time scales - systems with disparate masses
-
Tuckerman ME, Berne BJ, Rossi A. Molecular-dynamics algorithm for multiple time scales - systems with disparate masses. J Chem Phys 1991;94:1465-1469.
-
(1991)
J Chem Phys
, vol.94
, pp. 1465-1469
-
-
Tuckerman, M.E.1
Berne, B.J.2
Rossi, A.3
-
70
-
-
1942423619
-
MMTB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
-
Feig M, Karanicolas J, Brooks III CL, MMTB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:337-395.
-
(2004)
J Mol Graph Model
, vol.22
, pp. 337-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks III, C.L.3
-
72
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.F.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
73
-
-
33645941402
-
The OPLS potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin
-
Jorgensen WL, Tiradorives J. The OPLS potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin. J Am Chem Soc 1988;110:1666-1671.
-
(1988)
J Am Chem Soc
, vol.110
, pp. 1666-1671
-
-
Jorgensen, W.L.1
Tiradorives, J.2
-
74
-
-
0346971105
-
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 2004;25:265-284.
-
(2004)
J Comput Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
75
-
-
0037089017
-
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators
-
Gallicchio E, Zhang L, Levy R. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 2002;23:517-529.
-
(2002)
J Comput Chem
, vol.23
, pp. 517-529
-
-
Gallicchio, E.1
Zhang, L.2
Levy, R.3
-
76
-
-
40549104236
-
-
Schrodinger Inc. GLIDE. New York: Schrodinger Inc; 2004.
-
Schrodinger Inc. GLIDE. New York: Schrodinger Inc; 2004.
-
-
-
-
77
-
-
0033982936
-
-
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.
-
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.
-
-
-
-
78
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006;34:D354-D357.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
80
-
-
27744572136
-
A methodology for efficiently sampling the conformational space of molecular structures
-
Lee A, Streinu H, Brock O. A methodology for efficiently sampling the conformational space of molecular structures. Phys Biol 2005;2:s118-s125.
-
(2005)
Phys Biol
, vol.2
-
-
Lee, A.1
Streinu, H.2
Brock, O.3
-
81
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug design
-
Carlson HA. Protein flexibility is an important component of structure-based drug design. Curr Pharm Des 2002;8:1571-1578.
-
(2002)
Curr Pharm Des
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
82
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei B, Weaver L, Ferrari A, Matthews B, Shoichet B. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004;337:1161-1182.
-
(2004)
J Mol Biol
, vol.337
, pp. 1161-1182
-
-
Wei, B.1
Weaver, L.2
Ferrari, A.3
Matthews, B.4
Shoichet, B.5
-
83
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
Huang S, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007;66:399-421.
-
(2007)
Proteins
, vol.66
, pp. 399-421
-
-
Huang, S.1
Zou, X.2
|