-
1
-
-
0030793767
-
De Novo Protein Design: Fully Automated Sequence Selection
-
Dahiyat BI, Mayo SL, (1997) De Novo Protein Design: Fully Automated Sequence Selection. Science 278: 82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
2
-
-
33748207212
-
Configurational-bias sampling technique for predicting side-chain conformations in proteins
-
Jain T, (2006) Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Science 15: 2029-2039.
-
(2006)
Protein Science
, vol.15
, pp. 2029-2039
-
-
Jain, T.1
-
3
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195.
-
(2008)
Nature
, vol.453
, pp. 190-195
-
-
Rothlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
DeChancie, J.5
-
4
-
-
79956017135
-
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
-
Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
-
(2011)
Science
, vol.332
, pp. 816-821
-
-
Fleishman, S.J.1
Whitehead, T.A.2
Ekiert, D.C.3
Dreyfus, C.4
Corn, J.E.5
-
5
-
-
0026686436
-
Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]
-
Milton RC, Milton SC, Kent SB, (1992) Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]. Science 256: 1445-1448.
-
(1992)
Science
, vol.256
, pp. 1445-1448
-
-
Milton, R.C.1
Milton, S.C.2
Kent, S.B.3
-
6
-
-
1842502994
-
Enfuvirtide: a fusion inhibitor for the treatment of HIV infection
-
Fung HB, Guo Y, (2004) Enfuvirtide: a fusion inhibitor for the treatment of HIV infection. Clin Ther 26: 352-378.
-
(2004)
Clin Ther
, vol.26
, pp. 352-378
-
-
Fung, H.B.1
Guo, Y.2
-
7
-
-
0042208406
-
phi-Values beyond the ribosomally encoded amino acids: kinetic and thermodynamic consequences of incorporating trifluoromethyl amino acids in a globular protein
-
Horng JC, Raleigh DP, (2003) phi-Values beyond the ribosomally encoded amino acids: kinetic and thermodynamic consequences of incorporating trifluoromethyl amino acids in a globular protein. J Am Chem Soc 125: 9286-9287.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9286-9287
-
-
Horng, J.C.1
Raleigh, D.P.2
-
8
-
-
0025262173
-
Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure
-
Hendrickson WA, Horton JR, LeMaster DM, (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9: 1665-1672.
-
(1990)
EMBO J
, vol.9
, pp. 1665-1672
-
-
Hendrickson, W.A.1
Horton, J.R.2
LeMaster, D.M.3
-
9
-
-
66249139193
-
Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature
-
Banerjee R, Chattopadhyay S, Basu G, (2009) Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. Proteins 76: 184-200.
-
(2009)
Proteins
, vol.76
, pp. 184-200
-
-
Banerjee, R.1
Chattopadhyay, S.2
Basu, G.3
-
10
-
-
79961117960
-
Enhanced refoldability and thermoactivity of fluorinated phosphotriesterase
-
Baker PJ, Montclare JK, (2011) Enhanced refoldability and thermoactivity of fluorinated phosphotriesterase. Chembiochem 12: 1845-1848.
-
(2011)
Chembiochem
, vol.12
, pp. 1845-1848
-
-
Baker, P.J.1
Montclare, J.K.2
-
11
-
-
2942568222
-
Unimod: Protein modifications for mass spectrometry
-
Creasy DM, Cottrell JS, (2004) Unimod: Protein modifications for mass spectrometry. PROTEOMICS 4: 1534-1536.
-
(2004)
PROTEOMICS
, vol.4
, pp. 1534-1536
-
-
Creasy, D.M.1
Cottrell, J.S.2
-
12
-
-
2942564448
-
The RESID Database of Protein Modifications as a resource and annotation tool
-
Garavelli JS, (2004) The RESID Database of Protein Modifications as a resource and annotation tool. PROTEOMICS 4: 1527-1533.
-
(2004)
PROTEOMICS
, vol.4
, pp. 1527-1533
-
-
Garavelli, J.S.1
-
13
-
-
2942598149
-
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
-
Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B, (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. PROTEOMICS 4: 1551-1561.
-
(2004)
PROTEOMICS
, vol.4
, pp. 1551-1561
-
-
Hornbeck, P.V.1
Chabra, I.2
Kornhauser, J.M.3
Skrzypek, E.4
Zhang, B.5
-
14
-
-
0025963803
-
Selenocysteine: the 21st amino acid
-
Bock A, Forchhammer K, Heider J, Leinfelder W, Sawers G, et al. (1991) Selenocysteine: the 21st amino acid. Mol Microbiol 5: 515-520.
-
(1991)
Mol Microbiol
, vol.5
, pp. 515-520
-
-
Bock, A.1
Forchhammer, K.2
Heider, J.3
Leinfelder, W.4
Sawers, G.5
-
15
-
-
0037166006
-
Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA
-
Srinivasan G, James CM, Krzycki JA, (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296: 1459-1462.
-
(2002)
Science
, vol.296
, pp. 1459-1462
-
-
Srinivasan, G.1
James, C.M.2
Krzycki, J.A.3
-
17
-
-
44349127313
-
Using quantum mechanics to improve estimates of amino acid side chain rotamer energies
-
Renfrew PD, Butterfoss GL, Kuhlman B, (2008) Using quantum mechanics to improve estimates of amino acid side chain rotamer energies. Proteins 71: 1637-1646.
-
(2008)
Proteins
, vol.71
, pp. 1637-1646
-
-
Renfrew, P.D.1
Butterfoss, G.L.2
Kuhlman, B.3
-
18
-
-
78650905964
-
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-574.
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
-
19
-
-
1642464839
-
Protein Structure Prediction Using Rosetta
-
Academic Press
-
Rohl CA, Strauss CEM, Misura KMS, Baker D, Brand L, et al. (2004) Protein Structure Prediction Using Rosetta. pp. 66-93-66-93 Numerical Computer Methods, Part D: Academic Press.
-
(2004)
Numerical Computer Methods
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Misura, K.M.S.3
Baker, D.4
Brand, L.5
-
21
-
-
68349104348
-
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
-
Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Meth 6: 551-552.
-
(2009)
Nat Meth
, vol.6
, pp. 551-552
-
-
Mandell, D.J.1
Coutsias, E.A.2
Kortemme, T.3
-
23
-
-
79952608525
-
Accurate bond and angle parameters for X-ray protein structure refinement
-
Engh RA, Huber R, (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica Section A 47: 392-400.
-
(1991)
Acta Crystallographica Section A
, vol.47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
25
-
-
0038337815
-
The calpain system
-
Goll DE, Thompson VF, Li H, Wei W, Cong J, (2003) The calpain system. Physiol Rev 83: 731-801.
-
(2003)
Physiol Rev
, vol.83
, pp. 731-801
-
-
Goll, D.E.1
Thompson, V.F.2
Li, H.3
Wei, W.4
Cong, J.5
-
26
-
-
33644897573
-
Calpain inhibition: a therapeutic strategy targeting multiple disease states
-
Carragher NO, (2006) Calpain inhibition: a therapeutic strategy targeting multiple disease states. Curr Pharm Des 12: 615-638.
-
(2006)
Curr Pharm Des
, vol.12
, pp. 615-638
-
-
Carragher, N.O.1
-
27
-
-
33748902211
-
The therapeutic potential of the calpain family: new aspects
-
Saez ME, Ramirez-Lorca R, Moron FJ, Ruiz A, (2006) The therapeutic potential of the calpain family: new aspects. Drug Discov Today 11: 917-923.
-
(2006)
Drug Discov Today
, vol.11
, pp. 917-923
-
-
Saez, M.E.1
Ramirez-Lorca, R.2
Moron, F.J.3
Ruiz, A.4
-
28
-
-
79955458657
-
The calpain system and cancer
-
Storr SJ, Carragher NO, Frame MC, Parr T, Martin SG, (2011) The calpain system and cancer. Nat Rev Cancer 11: 364-374.
-
(2011)
Nat Rev Cancer
, vol.11
, pp. 364-374
-
-
Storr, S.J.1
Carragher, N.O.2
Frame, M.C.3
Parr, T.4
Martin, S.G.5
-
29
-
-
56749172400
-
Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin
-
Hanna RA, Campbell RL, Davies PL, (2008) Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. Nature 456: 409-412.
-
(2008)
Nature
, vol.456
, pp. 409-412
-
-
Hanna, R.A.1
Campbell, R.L.2
Davies, P.L.3
-
30
-
-
56749143763
-
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains
-
Moldoveanu T, Gehring K, Green DR, (2008) Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains. Nature 456: 404-408.
-
(2008)
Nature
, vol.456
, pp. 404-408
-
-
Moldoveanu, T.1
Gehring, K.2
Green, D.R.3
-
31
-
-
0037453230
-
A Structural Model for the Inhibition of Calpain by Calpastatin: Crystal Structures of the Native Domain VI of Calpain and its Complexes with Calpastatin Peptide and a Small Molecule Inhibitor
-
Todd B, Moore D, Deivanayagam CCS, Lin G-d, Chattopadhyay D, et al. (2003) A Structural Model for the Inhibition of Calpain by Calpastatin: Crystal Structures of the Native Domain VI of Calpain and its Complexes with Calpastatin Peptide and a Small Molecule Inhibitor. Journal of Molecular Biology 328: 131-146.
-
(2003)
Journal of Molecular Biology
, vol.328
, pp. 131-146
-
-
Todd, B.1
Moore, D.2
Deivanayagam, C.C.S.3
Lin, G.-d.4
Chattopadhyay, D.5
-
33
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M, (1999) Effective energy function for proteins in solution. Proteins: Structure, Function, and Genetics 35: 133-152.
-
(1999)
Proteins: Structure, Function, and Genetics
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
34
-
-
0037470581
-
An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes
-
Kortemme T, Morozov AV, Baker D, (2003) An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes. Journal of Molecular Biology 326: 1239-1259.
-
(2003)
Journal of Molecular Biology
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
35
-
-
24944493938
-
Toward High-Resolution de Novo Structure Prediction for Small Proteins
-
Bradley P, Misura KMS, Baker D, (2005) Toward High-Resolution de Novo Structure Prediction for Small Proteins. Science 309: 1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
36
-
-
0345306764
-
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. Science 302: 1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
-
37
-
-
0031727544
-
Protein sidechain conformer prediction: a test of the energy function
-
Petrella RJ, Lazaridis T, Karplus M, (1998) Protein sidechain conformer prediction: a test of the energy function. Folding and Design 3: 353-377.
-
(1998)
Folding and Design
, vol.3
, pp. 353-377
-
-
Petrella, R.J.1
Lazaridis, T.2
Karplus, M.3
-
38
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry 4: 187-217.
-
(1983)
Journal of Computational Chemistry
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
-
39
-
-
0043180474
-
PISCES: a protein sequence culling server
-
Wang G, Dunbrack RL Jr, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
40
-
-
33846630833
-
SODOCK: Swarm optimization for highly flexible protein-ligand docking
-
Chen HM, Liu BF, Huang HL, Hwang SF, Ho SY, (2007) SODOCK: Swarm optimization for highly flexible protein-ligand docking. Journal of Computational Chemistry 28: 612-623.
-
(2007)
Journal of Computational Chemistry
, vol.28
, pp. 612-623
-
-
Chen, H.M.1
Liu, B.F.2
Huang, H.L.3
Hwang, S.F.4
Ho, S.Y.5
-
43
-
-
0035845509
-
Conversion of monomeric protein L to an obligate dimer by computational protein design
-
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D, (2001) Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc Natl Acad Sci U S A 98: 10687-10691.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 10687-10691
-
-
Kuhlman, B.1
O'Neill, J.W.2
Kim, D.E.3
Zhang, K.Y.4
Baker, D.5
-
44
-
-
0034663722
-
The penultimate rotamer library
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (2000) The penultimate rotamer library. Proteins: Structure, Function, and Bioinformatics 40: 389-408.
-
(2000)
Proteins: Structure, Function, and Bioinformatics
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
45
-
-
0033582329
-
Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
-
Lovell SC, Word JM, Richardson JS, Richardson DC, (1999) Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proceedings of the National Academy of Sciences of the United States of America 96: 400-405.
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, pp. 400-405
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
46
-
-
0034789373
-
Labelled alpha-methyl-L-tryptophan as a tracer for the study of the brain serotonergic system
-
Diksic M, (2001) Labelled alpha-methyl-L-tryptophan as a tracer for the study of the brain serotonergic system. J Psychiatry Neurosci 26: 293-303.
-
(2001)
J Psychiatry Neurosci
, vol.26
, pp. 293-303
-
-
Diksic, M.1
-
47
-
-
69249158062
-
Computational design of affinity and specificity at protein-protein interfaces
-
Karanicolas J, Kuhlman B, (2009) Computational design of affinity and specificity at protein-protein interfaces. Curr Opin Struct Biol 19: 458-463.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 458-463
-
-
Karanicolas, J.1
Kuhlman, B.2
-
48
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov GG, Shapovalov MV, Dunbrack LD Jr, (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins: Structure, Function, and Bioinformatics 77: 778-795.
-
(2009)
Proteins: Structure, Function, and Bioinformatics
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack Jr., L.D.3
-
49
-
-
34548550463
-
An object-oriented library for computational protein design
-
Chowdry AB, Reynolds KA, Hanes MS, Voorhies M, Pokala N, et al. (2007) An object-oriented library for computational protein design. J Comput Chem 28: 2378-2388.
-
(2007)
J Comput Chem
, vol.28
, pp. 2378-2388
-
-
Chowdry, A.B.1
Reynolds, K.A.2
Hanes, M.S.3
Voorhies, M.4
Pokala, N.5
-
50
-
-
54049086941
-
Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms
-
Ho B, Agard D, (2008) Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms. BMC Structural Biology 8: 41-41.
-
(2008)
BMC Structural Biology
, vol.8
, pp. 41
-
-
Ho, B.1
Agard, D.2
-
51
-
-
70450202382
-
A preliminary survey of the peptoid folding landscape
-
Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R, (2009) A preliminary survey of the peptoid folding landscape. J Am Chem Soc 131: 16798-16807.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 16798-16807
-
-
Butterfoss, G.L.1
Renfrew, P.D.2
Kuhlman, B.3
Kirshenbaum, K.4
Bonneau, R.5
-
52
-
-
0029894733
-
Alpha-mercaptoacrylic acid derivatives as novel selective calpain inhibitors
-
Wang KK, Posner A, Raser KJ, Buroker-Kilgore M, Nath R, et al. (1996) Alpha-mercaptoacrylic acid derivatives as novel selective calpain inhibitors. Adv Exp Med Biol 389: 95-101.
-
(1996)
Adv Exp Med Biol
, vol.389
, pp. 95-101
-
-
Wang, K.K.1
Posner, A.2
Raser, K.J.3
Buroker-Kilgore, M.4
Nath, R.5
|