-
1
-
-
33846515095
-
Thermodynamics of neutral protein evolution
-
Bloom JD, Raval A, Wilke CO, (2007) Thermodynamics of neutral protein evolution. Genetics 175: 255-266.
-
(2007)
Genetics
, vol.175
, pp. 255-266
-
-
Bloom, J.D.1
Raval, A.2
Wilke, C.O.3
-
2
-
-
1842835981
-
Stability and the evolvability of function in a model protein
-
Bloom JD, Wilke CO, Arnold FH, Adami C, (2004) Stability and the evolvability of function in a model protein. Biophys J 86: 2758-2764.
-
(2004)
Biophys J
, vol.86
, pp. 2758-2764
-
-
Bloom, J.D.1
Wilke, C.O.2
Arnold, F.H.3
Adami, C.4
-
4
-
-
0037968852
-
Functional divergence in protein (family) sequence evolution
-
Gu X, (2003) Functional divergence in protein (family) sequence evolution. Genetica 118: 133-141.
-
(2003)
Genetica
, vol.118
, pp. 133-141
-
-
Gu, X.1
-
5
-
-
84863639111
-
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
-
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C, (2012) Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput Biol 8: e1002514.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Altenhoff, A.M.1
Studer, R.A.2
Robinson-Rechavi, M.3
Dessimoz, C.4
-
6
-
-
0344837306
-
Conservation of electrostatic properties within enzyme families and superfamilies
-
Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S, (2003) Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry 42: 3464-3473.
-
(2003)
Biochemistry
, vol.42
, pp. 3464-3473
-
-
Livesay, D.R.1
Jambeck, P.2
Rojnuckarin, A.3
Subramaniam, S.4
-
7
-
-
17744397525
-
The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins
-
Livesay DR, La D, (2005) The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins. Protein Sci 14: 1158-1170.
-
(2005)
Protein Sci
, vol.14
, pp. 1158-1170
-
-
Livesay, D.R.1
La, D.2
-
8
-
-
77956246214
-
Antibiotic discovery in the twenty-first century: current trends and future perspectives
-
Donadio S, Maffioli S, Monciardini P, Sosio M, Jabes D, (2010) Antibiotic discovery in the twenty-first century: current trends and future perspectives. J Antibiot (Tokyo) 63: 423-430.
-
(2010)
J Antibiot (Tokyo)
, vol.63
, pp. 423-430
-
-
Donadio, S.1
Maffioli, S.2
Monciardini, P.3
Sosio, M.4
Jabes, D.5
-
9
-
-
0024039854
-
An enzyme from bacteria able to destroy penicillin. 1940
-
Abraham EP, Chain E, (1988) An enzyme from bacteria able to destroy penicillin. 1940. Rev Infect Dis 10: 677-678.
-
(1988)
Rev Infect Dis
, vol.10
, pp. 677-678
-
-
Abraham, E.P.1
Chain, E.2
-
11
-
-
0043127209
-
Structural aspects for evolution of beta-lactamases from penicillin-binding proteins
-
Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S, (2003) Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc 125: 9612-9618.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9612-9618
-
-
Meroueh, S.O.1
Minasov, G.2
Lee, W.3
Shoichet, B.K.4
Mobashery, S.5
-
13
-
-
0242322614
-
Extended-spectrum beta-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type beta-lactamases
-
Paterson DL, Hujer KM, Hujer AM, Yeiser B, Bonomo MD, et al. (2003) Extended-spectrum beta-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type beta-lactamases. Antimicrob Agents Chemother 47: 3554-3560.
-
(2003)
Antimicrob Agents Chemother
, vol.47
, pp. 3554-3560
-
-
Paterson, D.L.1
Hujer, K.M.2
Hujer, A.M.3
Yeiser, B.4
Bonomo, M.D.5
-
14
-
-
0030835823
-
Detection and clinical significance of extended-spectrum beta-lactamases in a tertiary-care medical center
-
Emery CL, Weymouth LA, (1997) Detection and clinical significance of extended-spectrum beta-lactamases in a tertiary-care medical center. J Clin Microbiol 35: 2061-2067.
-
(1997)
J Clin Microbiol
, vol.35
, pp. 2061-2067
-
-
Emery, C.L.1
Weymouth, L.A.2
-
15
-
-
33646436194
-
Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase
-
Kim JY, Jung HI, An YJ, Lee JH, Kim SJ, et al. (2006) Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase. Mol Microbiol 60: 907-916.
-
(2006)
Mol Microbiol
, vol.60
, pp. 907-916
-
-
Kim, J.Y.1
Jung, H.I.2
An, Y.J.3
Lee, J.H.4
Kim, S.J.5
-
16
-
-
14844362964
-
Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity
-
Fisher JF, Meroueh SO, Mobashery S, (2005) Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 105: 395-424.
-
(2005)
Chem Rev
, vol.105
, pp. 395-424
-
-
Fisher, J.F.1
Meroueh, S.O.2
Mobashery, S.3
-
17
-
-
0029071785
-
A functional classification scheme for beta-lactamases and its correlation with molecular structure
-
Bush K, Jacoby GA, Medeiros AA, (1995) A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 39: 1211-1233.
-
(1995)
Antimicrob Agents Chemother
, vol.39
, pp. 1211-1233
-
-
Bush, K.1
Jacoby, G.A.2
Medeiros, A.A.3
-
18
-
-
0028706435
-
The structures and catalytic mechanisms of active-site serine beta-lactamases
-
Lamotte-Brasseur J, Knox J, Kelly JA, Charlier P, Fonze E, et al. (1994) The structures and catalytic mechanisms of active-site serine beta-lactamases. Biotechnol Genet Eng Rev 12: 189-230.
-
(1994)
Biotechnol Genet Eng Rev
, vol.12
, pp. 189-230
-
-
Lamotte-Brasseur, J.1
Knox, J.2
Kelly, J.A.3
Charlier, P.4
Fonze, E.5
-
19
-
-
0025647444
-
Site-directed mutagenesis of beta-lactamase I. Single and double mutants of Glu-166 and Lys-73
-
Gibson RM, Christensen H, Waley SG, (1990) Site-directed mutagenesis of beta-lactamase I. Single and double mutants of Glu-166 and Lys-73. Biochem J 272: 613-619.
-
(1990)
Biochem J
, vol.272
, pp. 613-619
-
-
Gibson, R.M.1
Christensen, H.2
Waley, S.G.3
-
20
-
-
0026504625
-
Streptomyces albus G serine beta-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes
-
Lamotte-Brasseur J, Jacob-Dubuisson F, Dive G, Frere JM, Ghuysen JM, (1992) Streptomyces albus G serine beta-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes. Biochem J 282 (Pt 1):: 189-195.
-
(1992)
Biochem J
, vol.282
, Issue.Pt 1
, pp. 189-195
-
-
Lamotte-Brasseur, J.1
Jacob-Dubuisson, F.2
Dive, G.3
Frere, J.M.4
Ghuysen, J.M.5
-
21
-
-
0025768209
-
Mechanism of acyl transfer by the class A serine beta-lactamase of Streptomyces albus G
-
Lamotte-Brasseur J, Dive G, Dideberg O, Charlier P, Frere JM, et al. (1991) Mechanism of acyl transfer by the class A serine beta-lactamase of Streptomyces albus G. Biochem J 279 (Pt 1):: 213-221.
-
(1991)
Biochem J
, vol.279
, Issue.Pt 1
, pp. 213-221
-
-
Lamotte-Brasseur, J.1
Dive, G.2
Dideberg, O.3
Charlier, P.4
Frere, J.M.5
-
22
-
-
0029760859
-
Structure-based design of a potent transition state analogue for TEM-1 bold beta-lactamase
-
Strynadka NCJ, Martin R, Jensen SE, Gold M, Jones JB, (1996) Structure-based design of a potent transition state analogue for TEM-1 bold beta-lactamase. Nature Struct Biol 3: 688-695.
-
(1996)
Nature Struct Biol
, vol.3
, pp. 688-695
-
-
Strynadka, N.C.J.1
Martin, R.2
Jensen, S.E.3
Gold, M.4
Jones, J.B.5
-
23
-
-
0001478191
-
Penicillin-binding and degrading enzymes
-
Herzberg O, Moult J, (1991) Penicillin-binding and degrading enzymes. Curr Opin Struct Biol 1: 946-953.
-
(1991)
Curr Opin Struct Biol
, vol.1
, pp. 946-953
-
-
Herzberg, O.1
Moult, J.2
-
24
-
-
0026801518
-
Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution
-
Strynadka NC, Adachi H, Jensen SE, Johns K, Sielecki A, et al. (1992) Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution. Nature 359: 700-705.
-
(1992)
Nature
, vol.359
, pp. 700-705
-
-
Strynadka, N.C.1
Adachi, H.2
Jensen, S.E.3
Johns, K.4
Sielecki, A.5
-
25
-
-
0025801845
-
Site-directed mutants, at position 166, of RTEM-1 beta-lactamase that form a stable acyl-enzyme intermediate with penicillin
-
Adachi H, Ohta T, Matsuzawa H, (1991) Site-directed mutants, at position 166, of RTEM-1 beta-lactamase that form a stable acyl-enzyme intermediate with penicillin. J Biol Chem 266: 3186-3191.
-
(1991)
J Biol Chem
, vol.266
, pp. 3186-3191
-
-
Adachi, H.1
Ohta, T.2
Matsuzawa, H.3
-
26
-
-
0029644936
-
Electrostatic analysis of TEM1 β-lactamase: effect of substrate binding, steep potential gradients and consequences of site-directed mutations
-
Swarén P, Maveyraud L, Guillet V, Masson J-M, Mourey L, et al. (1995) Electrostatic analysis of TEM1 β-lactamase: effect of substrate binding, steep potential gradients and consequences of site-directed mutations. Structure 3: 603-613.
-
(1995)
Structure
, vol.3
, pp. 603-613
-
-
Swarén, P.1
Maveyraud, L.2
Guillet, V.3
Masson, J.-M.4
Mourey, L.5
-
27
-
-
0028802117
-
Contribution of mutant analysis to the understanding of enzyme catalysis: the case of class A beta-lactamases
-
Matagne A, Frere JM, (1995) Contribution of mutant analysis to the understanding of enzyme catalysis: the case of class A beta-lactamases. Biochim Biophys Acta 1246: 109-127.
-
(1995)
Biochim Biophys Acta
, vol.1246
, pp. 109-127
-
-
Matagne, A.1
Frere, J.M.2
-
28
-
-
0029944652
-
The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme
-
Damblon C, Raquet X, Lian LY, Lamotte-Brasseur J, Fonze E, et al. (1996) The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. Proceedings of the National Academy of Sciences 93: 1747-1752.
-
(1996)
Proceedings of the National Academy of Sciences
, vol.93
, pp. 1747-1752
-
-
Damblon, C.1
Raquet, X.2
Lian, L.Y.3
Lamotte-Brasseur, J.4
Fonze, E.5
-
29
-
-
0025954720
-
Comparison of the sequences of class A beta-lactamases and of the secondary structure elements of penicillin-recognizing proteins
-
Joris B, Ledent P, Dideberg O, Fonze E, Lamotte-Brasseur J, et al. (1991) Comparison of the sequences of class A beta-lactamases and of the secondary structure elements of penicillin-recognizing proteins. Antimicrob Agents Chemother 35: 2294-2301.
-
(1991)
Antimicrob Agents Chemother
, vol.35
, pp. 2294-2301
-
-
Joris, B.1
Ledent, P.2
Dideberg, O.3
Fonze, E.4
Lamotte-Brasseur, J.5
-
30
-
-
0026049801
-
Serine beta-lactamases and penicillin-binding proteins
-
Ghuysen JM, (1991) Serine beta-lactamases and penicillin-binding proteins. Annu Rev Microbiol 45: 37-67.
-
(1991)
Annu Rev Microbiol
, vol.45
, pp. 37-67
-
-
Ghuysen, J.M.1
-
31
-
-
0023976519
-
The active-site-serine penicillin-recognizing enzymes as members of the Streptomyces R61 DD-peptidase family
-
Joris B, Ghuysen JM, Dive G, Renard A, Dideberg O, et al. (1988) The active-site-serine penicillin-recognizing enzymes as members of the Streptomyces R61 DD-peptidase family. Biochem J 250: 313-324.
-
(1988)
Biochem J
, vol.250
, pp. 313-324
-
-
Joris, B.1
Ghuysen, J.M.2
Dive, G.3
Renard, A.4
Dideberg, O.5
-
32
-
-
0028906105
-
Primary structure of OXA-3 and phylogeny of oxacillin-hydrolyzing class D beta-lactamases
-
Sanschagrin F, Couture F, Levesque RC, (1995) Primary structure of OXA-3 and phylogeny of oxacillin-hydrolyzing class D beta-lactamases. Antimicrob Agents Chemother 39: 887-893.
-
(1995)
Antimicrob Agents Chemother
, vol.39
, pp. 887-893
-
-
Sanschagrin, F.1
Couture, F.2
Levesque, R.C.3
-
33
-
-
0032726693
-
Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity
-
Blomberg N, Gabdoulline RR, Nilges M, Wade RC, (1999) Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. Proteins: Structure, Function, and Bioinformatics 37: 379-387.
-
(1999)
Proteins: Structure, Function, and Bioinformatics
, vol.37
, pp. 379-387
-
-
Blomberg, N.1
Gabdoulline, R.R.2
Nilges, M.3
Wade, R.C.4
-
34
-
-
0033923367
-
Rational design of faster associating and tighter binding protein complexes
-
Selzer T, Albeck S, Schreiber G, (2000) Rational design of faster associating and tighter binding protein complexes. Nat Struct Biol 7: 537-541.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 537-541
-
-
Selzer, T.1
Albeck, S.2
Schreiber, G.3
-
35
-
-
0035122917
-
Predicting the emergence of antibiotic resistance by directed evolution and structural analysis
-
Orencia MC, Yoon JS, Ness JE, Stemmer WP, Stevens RC, (2001) Predicting the emergence of antibiotic resistance by directed evolution and structural analysis. Nat Struct Biol 8: 238-242.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 238-242
-
-
Orencia, M.C.1
Yoon, J.S.2
Ness, J.E.3
Stemmer, W.P.4
Stevens, R.C.5
-
36
-
-
0036019341
-
Improving a circularly permuted TEM-1 beta-lactamase by directed evolution
-
Osuna J, Perez-Blancas A, Soberon X, (2002) Improving a circularly permuted TEM-1 beta-lactamase by directed evolution. Protein Eng 15: 463-470.
-
(2002)
Protein Eng
, vol.15
, pp. 463-470
-
-
Osuna, J.1
Perez-Blancas, A.2
Soberon, X.3
-
37
-
-
30344476409
-
Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
-
Livesay DR, Jacobs DJ, (2006) Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins 62: 130-143.
-
(2006)
Proteins
, vol.62
, pp. 130-143
-
-
Livesay, D.R.1
Jacobs, D.J.2
-
38
-
-
51749092455
-
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
-
Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ, (2008) Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chem Cent J 2: 17.
-
(2008)
Chem Cent J
, vol.2
, pp. 17
-
-
Livesay, D.R.1
Huynh, D.H.2
Dallakyan, S.3
Jacobs, D.J.4
-
39
-
-
33646033429
-
Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model
-
Jacobs DJ, Livesay DR, Hules J, Tasayco ML, (2006) Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. J Mol Biol 358: 882-904.
-
(2006)
J Mol Biol
, vol.358
, pp. 882-904
-
-
Jacobs, D.J.1
Livesay, D.R.2
Hules, J.3
Tasayco, M.L.4
-
40
-
-
66149154705
-
Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family
-
Mottonen JM, Xu M, Jacobs DJ, Livesay DR, (2009) Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins 75: 610-627.
-
(2009)
Proteins
, vol.75
, pp. 610-627
-
-
Mottonen, J.M.1
Xu, M.2
Jacobs, D.J.3
Livesay, D.R.4
-
41
-
-
79251478002
-
Predicting the melting point of human C-type lysozyme mutants
-
Verma D, Jacobs DJ, Livesay DR, (2010) Predicting the melting point of human C-type lysozyme mutants. Curr Protein Pept Sci 11: 562-572.
-
(2010)
Curr Protein Pept Sci
, vol.11
, pp. 562-572
-
-
Verma, D.1
Jacobs, D.J.2
Livesay, D.R.3
-
42
-
-
84861149876
-
Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged
-
Verma D, Jacobs DJ, Livesay DR, (2012) Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. PLoS Comput Biol 8: e1002409.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Verma, D.1
Jacobs, D.J.2
Livesay, D.R.3
-
43
-
-
33749007969
-
Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein
-
Savard PY, Gagne SM, (2006) Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein. Biochemistry 45: 11414-11424.
-
(2006)
Biochemistry
, vol.45
, pp. 11414-11424
-
-
Savard, P.Y.1
Gagne, S.M.2
-
44
-
-
77954466604
-
Investigation of TEM-1 and SHV-1 beta-lactamase ligand binding
-
20-22 April 2010
-
Kanlikili P, Olmez E, Budeyri N, Akbulut BS, (2010) Investigation of TEM-1 and SHV-1 beta-lactamase ligand binding. 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), 2010. 20-22 April 2010. pp. 167-172.
-
(2010)
5th International Symposium on Health Informatics and Bioinformatics (HIBIT), 2010
, pp. 167-172
-
-
Kanlikili, P.1
Olmez, E.2
Budeyri, N.3
Akbulut, B.S.4
-
45
-
-
72249091122
-
Multiple molecular dynamics simulations of TEM beta-lactamase: dynamics and water binding of the omega-loop
-
Bos F, Pleiss J, (2009) Multiple molecular dynamics simulations of TEM beta-lactamase: dynamics and water binding of the omega-loop. Biophys J 97: 2550-2558.
-
(2009)
Biophys J
, vol.97
, pp. 2550-2558
-
-
Bos, F.1
Pleiss, J.2
-
46
-
-
0032502332
-
Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase
-
Banerjee S, Pieper U, Kapadia G, Pannell LK, Herzberg O, (1998) Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase. Biochemistry 37: 3286-3296.
-
(1998)
Biochemistry
, vol.37
, pp. 3286-3296
-
-
Banerjee, S.1
Pieper, U.2
Kapadia, G.3
Pannell, L.K.4
Herzberg, O.5
-
47
-
-
65349195698
-
Molecular docking and ligand specificity in fragment-based inhibitor discovery
-
Chen Y, Shoichet BK, (2009) Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol 5: 358-364.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 358-364
-
-
Chen, Y.1
Shoichet, B.K.2
-
48
-
-
0036752271
-
Using steric hindrance to design new inhibitors of class C beta-lactamases
-
Trehan I, Morandi F, Blaszczak LC, Shoichet BK, (2002) Using steric hindrance to design new inhibitors of class C beta-lactamases. Chem Biol 9: 971-980.
-
(2002)
Chem Biol
, vol.9
, pp. 971-980
-
-
Trehan, I.1
Morandi, F.2
Blaszczak, L.C.3
Shoichet, B.K.4
-
49
-
-
16244415566
-
Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability
-
Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R, (2005) Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability. J Mol Biol 348: 349-362.
-
(2005)
J Mol Biol
, vol.348
, pp. 349-362
-
-
Chen, Y.1
Delmas, J.2
Sirot, J.3
Shoichet, B.4
Bonnet, R.5
-
50
-
-
77958469848
-
Allosteric response is both conserved and variable across three CheY orthologs
-
Mottonen JM, Jacobs DJ, Livesay DR, (2010) Allosteric response is both conserved and variable across three CheY orthologs. Biophys J 99: 2245-2254.
-
(2010)
Biophys J
, vol.99
, pp. 2245-2254
-
-
Mottonen, J.M.1
Jacobs, D.J.2
Livesay, D.R.3
-
51
-
-
77249152215
-
TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance
-
Fisette O, Morin S, Savard PY, Lague P, Gagne SM, (2010) TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance. Biophys J 98: 637-645.
-
(2010)
Biophys J
, vol.98
, pp. 637-645
-
-
Fisette, O.1
Morin, S.2
Savard, P.Y.3
Lague, P.4
Gagne, S.M.5
-
52
-
-
80052398961
-
Increased structural flexibility at the active site of a fluorophore-conjugated beta-lactamase distinctively impacts its binding toward diverse cephalosporin antibiotics
-
Wong WT, Chan KC, So PK, Yap HK, Chung WH, et al. (2011) Increased structural flexibility at the active site of a fluorophore-conjugated beta-lactamase distinctively impacts its binding toward diverse cephalosporin antibiotics. J Biol Chem 286: 31771-31780.
-
(2011)
J Biol Chem
, vol.286
, pp. 31771-31780
-
-
Wong, W.T.1
Chan, K.C.2
So, P.K.3
Yap, H.K.4
Chung, W.H.5
-
53
-
-
23144457576
-
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368-371.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
-
55
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
56
-
-
1542285840
-
Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
-
Jacobs DJ, Dallakyan S, Wood GG, Heckathorne A, (2003) Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys Rev E Stat Nonlin Soft Matter Phys 68: 061109.
-
(2003)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.68
, pp. 061109
-
-
Jacobs, D.J.1
Dallakyan, S.2
Wood, G.G.3
Heckathorne, A.4
-
57
-
-
72549119922
-
Helix/coil nucleation: a local response to global demands
-
Vorov OK, Livesay DR, Jacobs DJ, (2009) Helix/coil nucleation: a local response to global demands. Biophys J 97: 3000-3009.
-
(2009)
Biophys J
, vol.97
, pp. 3000-3009
-
-
Vorov, O.K.1
Livesay, D.R.2
Jacobs, D.J.3
-
58
-
-
79951828754
-
Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity
-
Vorov OK, Livesay DR, Jacobs DJ, (2011) Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Biophys J 100: 1129-1138.
-
(2011)
Biophys J
, vol.100
, pp. 1129-1138
-
-
Vorov, O.K.1
Livesay, D.R.2
Jacobs, D.J.3
-
59
-
-
0031281604
-
An algorithm for two-dimensional rigidity percolation: The pebble game
-
Jacobs DJ, Hendrickson B, (1997) An algorithm for two-dimensional rigidity percolation: The pebble game. J Comp Phys 137: 346-365.
-
(1997)
J Comp Phys
, vol.137
, pp. 346-365
-
-
Jacobs, D.J.1
Hendrickson, B.2
-
60
-
-
0035427398
-
Protein flexibility predictions using graph theory
-
Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF, (2001) Protein flexibility predictions using graph theory. Proteins 44: 150-165.
-
(2001)
Proteins
, vol.44
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.J.2
Kuhn, L.A.3
Thorpe, M.F.4
-
61
-
-
0000785338
-
Generic rigidity percolation: The pebble game
-
Jacobs DJ, Thorpe MF, (1995) Generic rigidity percolation: The pebble game. Phys Rev Lett 75: 4051-4054.
-
(1995)
Phys Rev Lett
, vol.75
, pp. 4051-4054
-
-
Jacobs, D.J.1
Thorpe, M.F.2
-
62
-
-
21244483843
-
Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
-
Jacobs DJ, Dallakyan S, (2005) Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys J 88: 903-915.
-
(2005)
Biophys J
, vol.88
, pp. 903-915
-
-
Jacobs, D.J.1
Dallakyan, S.2
-
63
-
-
6344223617
-
A flexible approach for understanding protein stability
-
Livesay DR, Dallakyan S, Wood GG, Jacobs DJ, (2004) A flexible approach for understanding protein stability. FEBS Lett 576: 468-476.
-
(2004)
FEBS Lett
, vol.576
, pp. 468-476
-
-
Livesay, D.R.1
Dallakyan, S.2
Wood, G.G.3
Jacobs, D.J.4
-
64
-
-
0343742614
-
Automated design of the surface positions of protein helices
-
Dahiyat BI, Gordon DB, Mayo SL, (1997) Automated design of the surface positions of protein helices. Protein Sci 6: 1333-1337.
-
(1997)
Protein Sci
, vol.6
, pp. 1333-1337
-
-
Dahiyat, B.I.1
Gordon, D.B.2
Mayo, S.L.3
-
65
-
-
0037432188
-
Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?
-
Fernandez A, Kardos J, Goto Y, (2003) Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation? FEBS Lett 536: 187-192.
-
(2003)
FEBS Lett
, vol.536
, pp. 187-192
-
-
Fernandez, A.1
Kardos, J.2
Goto, Y.3
-
66
-
-
0026766543
-
Differential scanning calorimetric study of the thermal unfolding of. beta.-lactamase I from Bacillus cereus
-
Arriaga P, Menendez M, Villacorta JM, Laynez J, (1992) Differential scanning calorimetric study of the thermal unfolding of. beta.-lactamase I from Bacillus cereus. Biochemistry 31: 6603-6607.
-
(1992)
Biochemistry
, vol.31
, pp. 6603-6607
-
-
Arriaga, P.1
Menendez, M.2
Villacorta, J.M.3
Laynez, J.4
-
67
-
-
0025271184
-
Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution
-
Moews PC, Knox JR, Dideberg O, Charlier P, Frere JM, (1990) Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution. Proteins 7: 156-171.
-
(1990)
Proteins
, vol.7
, pp. 156-171
-
-
Moews, P.C.1
Knox, J.R.2
Dideberg, O.3
Charlier, P.4
Frere, J.M.5
-
68
-
-
0026016867
-
Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution
-
Herzberg O, (1991) Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution. J Mol Biol 217: 701-719.
-
(1991)
J Mol Biol
, vol.217
, pp. 701-719
-
-
Herzberg, O.1
-
69
-
-
33745620493
-
Crystal structure of the Mycobacterium fortuitum class A beta-lactamase: structural basis for broad substrate specificity
-
Sauvage E, Fonze E, Quinting B, Galleni M, Frere JM, et al. (2006) Crystal structure of the Mycobacterium fortuitum class A beta-lactamase: structural basis for broad substrate specificity. Antimicrob Agents Chemother 50: 2516-2521.
-
(2006)
Antimicrob Agents Chemother
, vol.50
, pp. 2516-2521
-
-
Sauvage, E.1
Fonze, E.2
Quinting, B.3
Galleni, M.4
Frere, J.M.5
-
70
-
-
0033522376
-
Structure of the SHV-1 beta-lactamase
-
Kuzin AP, Nukaga M, Nukaga Y, Hujer AM, Bonomo RA, et al. (1999) Structure of the SHV-1 beta-lactamase. Biochemistry 38: 5720-5727.
-
(1999)
Biochemistry
, vol.38
, pp. 5720-5727
-
-
Kuzin, A.P.1
Nukaga, M.2
Nukaga, Y.3
Hujer, A.M.4
Bonomo, R.A.5
-
71
-
-
0037453313
-
Ultrahigh resolution structure of a class A beta-lactamase: on the mechanism and specificity of the extended-spectrum SHV-2 enzyme
-
Nukaga M, Mayama K, Hujer AM, Bonomo RA, Knox JR, (2003) Ultrahigh resolution structure of a class A beta-lactamase: on the mechanism and specificity of the extended-spectrum SHV-2 enzyme. J Mol Biol 328: 289-301.
-
(2003)
J Mol Biol
, vol.328
, pp. 289-301
-
-
Nukaga, M.1
Mayama, K.2
Hujer, A.M.3
Bonomo, R.A.4
Knox, J.R.5
-
72
-
-
0030836575
-
Sequence analysis and enzyme kinetics of the L2 serine beta-lactamase from Stenotrophomonas maltophilia
-
Walsh TR, MacGowan AP, Bennett PM, (1997) Sequence analysis and enzyme kinetics of the L2 serine beta-lactamase from Stenotrophomonas maltophilia. Antimicrob Agents Chemother 41: 1460-1464.
-
(1997)
Antimicrob Agents Chemother
, vol.41
, pp. 1460-1464
-
-
Walsh, T.R.1
MacGowan, A.P.2
Bennett, P.M.3
-
73
-
-
0035895310
-
Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies
-
Lim D, Sanschagrin F, Passmore L, De Castro L, Levesque RC, et al. (2001) Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies. Biochemistry 40: 395-402.
-
(2001)
Biochemistry
, vol.40
, pp. 395-402
-
-
Lim, D.1
Sanschagrin, F.2
Passmore, L.3
De Castro, L.4
Levesque, R.C.5
-
74
-
-
0036008512
-
Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens
-
Sougakoff W, L'Hermite G, Pernot L, Naas T, Guillet V, et al. (2002) Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens. Acta Crystallogr D Biol Crystallogr 58: 267-274.
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, pp. 267-274
-
-
Sougakoff, W.1
L'Hermite, G.2
Pernot, L.3
Naas, T.4
Guillet, V.5
-
75
-
-
15444338960
-
X-ray analysis of the NMC-A beta-lactamase at 1.64-A resolution, a class A carbapenemase with broad substrate specificity
-
Swaren P, Maveyraud L, Raquet X, Cabantous S, Duez C, et al. (1998) X-ray analysis of the NMC-A beta-lactamase at 1.64-A resolution, a class A carbapenemase with broad substrate specificity. J Biol Chem 273: 26714-26721.
-
(1998)
J Biol Chem
, vol.273
, pp. 26714-26721
-
-
Swaren, P.1
Maveyraud, L.2
Raquet, X.3
Cabantous, S.4
Duez, C.5
-
76
-
-
0027275788
-
Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution
-
Jelsch C, Mourey L, Masson JM, Samama JP, (1993) Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution. Proteins 16: 364-383.
-
(1993)
Proteins
, vol.16
, pp. 364-383
-
-
Jelsch, C.1
Mourey, L.2
Masson, J.M.3
Samama, J.P.4
-
77
-
-
0023388516
-
The crystal structure of the beta-lactamase of Streptomyces albus G at 0.3 nm resolution
-
Dideberg O, Charlier P, Wery JP, Dehottay P, Dusart J, et al. (1987) The crystal structure of the beta-lactamase of Streptomyces albus G at 0.3 nm resolution. Biochem J 245: 911-913.
-
(1987)
Biochem J
, vol.245
, pp. 911-913
-
-
Dideberg, O.1
Charlier, P.2
Wery, J.P.3
Dehottay, P.4
Dusart, J.5
-
78
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
79
-
-
0043180474
-
PISCES: a protein sequence culling server
-
Wang G, Dunbrack RL, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
80
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
81
-
-
84880841889
-
Multiple sequence and structural alignment in MOE
-
Kelly K, (1996) Multiple sequence and structural alignment in MOE. Chemical Computing Group.
-
(1996)
Chemical Computing Group
-
-
Kelly, K.1
-
82
-
-
84950632109
-
Objective Criteria for the Evaluation of Clustering Methods
-
Rand WM, (1971) Objective Criteria for the Evaluation of Clustering Methods. Journal of the American Statistical Association 66: 846-850.
-
(1971)
Journal of the American Statistical Association
, vol.66
, pp. 846-850
-
-
Rand, W.M.1
-
83
-
-
84863155751
-
Calculating ensemble averaged descriptions of protein rigidity without sampling
-
Gonzalez LC, Wang H, Livesay DR, Jacobs DJ, (2012) Calculating ensemble averaged descriptions of protein rigidity without sampling. PLoS ONE 7: e29176.
-
(2012)
PLoS ONE
, vol.7
-
-
Gonzalez, L.C.1
Wang, H.2
Livesay, D.R.3
Jacobs, D.J.4
-
84
-
-
77149165713
-
Updated functional classification of beta-lactamases
-
Bush K, Jacoby GA, (2010) Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 54: 969-976.
-
(2010)
Antimicrob Agents Chemother
, vol.54
, pp. 969-976
-
-
Bush, K.1
Jacoby, G.A.2
|