-
1
-
-
0035954729
-
Antibacterial agents based on the cyclic D,L-α-peptide architecture
-
Fernandez-Lopez, S., H. Kim, E. C. Choi, M. Delgado, J. R. Granja, A. Khasanov, K. Kraehenbuehl, G. Long, D. A. Weinberger, K. M. Wilcoxen, and M. R. Ghadiri. 2001. Antibacterial agents based on the cyclic D,L-α-peptide architecture. Nature. 412:452-455.
-
(2001)
Nature
, vol.412
, pp. 452-455
-
-
Fernandez-Lopez, S.1
Kim, H.2
Choi, E.C.3
Delgado, M.4
Granja, J.R.5
Khasanov, A.6
Kraehenbuehl, K.7
Long, G.8
Weinberger, D.A.9
Wilcoxen, K.M.10
Ghadiri, M.R.11
-
2
-
-
0035936156
-
Innate antimicrobial peptide protects the skin from invasive bacterial infection
-
Nizet, V., T. Ohtake, X. Lauth, J. Trowbridge, J. Rudisill, R. A. Dorschner, V. Pestonjamasp, J. Piranino, K. Huttner, and R. L. Gallo. 2001. Innate antimicrobial peptide protects the skin from invasive bacterial infection. Nature. 414:454-457.
-
(2001)
Nature
, vol.414
, pp. 454-457
-
-
Nizet, V.1
Ohtake, T.2
Lauth, X.3
Trowbridge, J.4
Rudisill, J.5
Dorschner, R.A.6
Pestonjamasp, V.7
Piranino, J.8
Huttner, K.9
Gallo, R.L.10
-
3
-
-
0037165196
-
Antimicrobial peptides of multicellular organisms
-
Zasloff, M. 2002. Antimicrobial peptides of multicellular organisms. Nature. 415:389-395.
-
(2002)
Nature
, vol.415
, pp. 389-395
-
-
Zasloff, M.1
-
4
-
-
0141799911
-
Defensins: Antimicrobial peptides of innate immunity
-
Ganz, T. 2003. Defensins: antimicrobial peptides of innate immunity. Nature. 3:710-720.
-
(2003)
Nature
, vol.3
, pp. 710-720
-
-
Ganz, T.1
-
5
-
-
27144504220
-
Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus
-
Mygind, P. H., R. L. Fischer, K. M. Schnorr, M. T. Hansen, C. P. Sönksen, S. Ludvigsen, D. Raventós, S. Buskov, B. Christensen, L. D. Maria, O. Taboureau, D. Yaver, S. G. Elvig-Jørgensen, M. V. Sørensen, B. E. Christensen, S. Kjærulff, N. Frimodt-Moller, R. I. Lehrer, M. Zasloff, and H.-H. Kristensen. 2005. Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature. 437:975-980.
-
(2005)
Nature
, vol.437
, pp. 975-980
-
-
Mygind, P.H.1
Fischer, R.L.2
Schnorr, K.M.3
Hansen, M.T.4
Sönksen, C.P.5
Ludvigsen, S.6
Raventós, D.7
Buskov, S.8
Christensen, B.9
Maria, L.D.10
Taboureau, O.11
Yaver, D.12
Elvig-Jørgensen, S.G.13
Sørensen, M.V.14
Christensen, B.E.15
Kjærulff, S.16
Frimodt-Moller, N.17
Lehrer, R.I.18
Zasloff, M.19
Kristensen, H.-H.20
more..
-
6
-
-
33750304297
-
A linguistic model for the rational design of antimicrobial peptides
-
Loose, C., K. Jensen, I. Rigoutsos, and G. Stephanopoulos. 2006. A linguistic model for the rational design of antimicrobial peptides. Nature. 443:867-869.
-
(2006)
Nature
, vol.443
, pp. 867-869
-
-
Loose, C.1
Jensen, K.2
Rigoutsos, I.3
Stephanopoulos, G.4
-
7
-
-
0035984978
-
A Clinical development of cationic antimicrobial peptides: From natural to novel antibiotics
-
Hancock, R. E., and A. Patrzykat. 2002. A Clinical development of cationic antimicrobial peptides: from natural to novel antibiotics. Curr. Drug Targets Infect. Disord. 2:79-83.
-
(2002)
Curr. Drug Targets Infect. Disord
, vol.2
, pp. 79-83
-
-
Hancock, R.E.1
Patrzykat, A.2
-
8
-
-
1642318503
-
Human β-defensin-2 functions as a chemotactic agent for tumor necrosis factor-α-treated human neutrophils
-
Niyonsaba, F., H. Ogawa, and I. Nagaoka. 2004. Human β-defensin-2 functions as a chemotactic agent for tumor necrosis factor-α-treated human neutrophils. Immunology. 111:273-281.
-
(2004)
Immunology
, vol.111
, pp. 273-281
-
-
Niyonsaba, F.1
Ogawa, H.2
Nagaoka, I.3
-
11
-
-
0034929327
-
Defensin antimicrobial peptides in the oral cavity
-
Dale, B., and S. Krisanaprakornkit. 2001. Defensin antimicrobial peptides in the oral cavity. J. Oral Pathol. Med. 30:321-327.
-
(2001)
J. Oral Pathol. Med
, vol.30
, pp. 321-327
-
-
Dale, B.1
Krisanaprakornkit, S.2
-
12
-
-
0035128459
-
Expression profile of human defensins and antimicrobial proteins in oral tissues
-
Dunsche, A., Y. Acil, R. Siebert, J. Harder, J. M. Schroder, and S. Jepsen. 2001. Expression profile of human defensins and antimicrobial proteins in oral tissues. J. Oral Pathol. Med. 30:154-158.
-
(2001)
J. Oral Pathol. Med
, vol.30
, pp. 154-158
-
-
Dunsche, A.1
Acil, Y.2
Siebert, R.3
Harder, J.4
Schroder, J.M.5
Jepsen, S.6
-
13
-
-
0030820726
-
A peptide antibiotic from human skin
-
Harder, J., J. Bartels, E. Christophers, and J.-M. Schröder. 1997. A peptide antibiotic from human skin. Nature. 387:861.
-
(1997)
Nature
, vol.387
, pp. 861
-
-
Harder, J.1
Bartels, J.2
Christophers, E.3
Schröder, J.-M.4
-
14
-
-
0025959114
-
Defensins: Endogenous antibiotic peptides of animal cells
-
Lehrer, R. I., T. Ganz, and M. E. Selsted. 1991. Defensins: endogenous antibiotic peptides of animal cells. Cell. 64:229-230.
-
(1991)
Cell
, vol.64
, pp. 229-230
-
-
Lehrer, R.I.1
Ganz, T.2
Selsted, M.E.3
-
15
-
-
0029819784
-
Paneth cell defensins: Endogenous peptide components of intestinal host defense
-
Ouellette, A. J., and M. E. Selsted. 1996. Paneth cell defensins: endogenous peptide components of intestinal host defense. FASEB J. 10:1280-1289.
-
(1996)
FASEB J
, vol.10
, pp. 1280-1289
-
-
Ouellette, A.J.1
Selsted, M.E.2
-
16
-
-
33746299143
-
Antimicrobial activities of human β-defensins against Bacillus species
-
Yadava, P., C. Zhang, J. Sun, and J. A. Hughes. 2006. Antimicrobial activities of human β-defensins against Bacillus species. Int. J. Antimicrob. Agents. 28:132-137.
-
(2006)
Int. J. Antimicrob. Agents
, vol.28
, pp. 132-137
-
-
Yadava, P.1
Zhang, C.2
Sun, J.3
Hughes, J.A.4
-
17
-
-
0037699589
-
Integrated structural, computational and experimental approach for lead optimization: Design of compstatin variants with improved activity
-
Klepeis, J. L., C. A. Floudas, D. Morikis, C. G. Tsokos, E. Argyropoulos, L. Spruce, and J. D. Lambris. 2003. Integrated structural, computational and experimental approach for lead optimization: design of compstatin variants with improved activity. J. Am. Chem. Soc. 125:8422-8423.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 8422-8423
-
-
Klepeis, J.L.1
Floudas, C.A.2
Morikis, D.3
Tsokos, C.G.4
Argyropoulos, E.5
Spruce, L.6
Lambris, J.D.7
-
18
-
-
3042785531
-
Design of peptide analogs with improved activity using a novel de novo protein design approach
-
Klepeis, J. L., C. A. Floudas, D. Morikis, C. G. Tsokos, and J. D. Lambris. 2004. Design of peptide analogs with improved activity using a novel de novo protein design approach. Ind. Eng. Chem. Res. 43: 3817-3826.
-
(2004)
Ind. Eng. Chem. Res
, vol.43
, pp. 3817-3826
-
-
Klepeis, J.L.1
Floudas, C.A.2
Morikis, D.3
Tsokos, C.G.4
Lambris, J.D.5
-
19
-
-
23944486752
-
Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design
-
Fung, H. K., S. Rao, C. A. Floudas, O. Prokopyev, P. M. Pardalos, and F. Rendl. 2005. Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design. J. Comb. Optim. 10:41-60.
-
(2005)
J. Comb. Optim
, vol.10
, pp. 41-60
-
-
Fung, H.K.1
Rao, S.2
Floudas, C.A.3
Prokopyev, O.4
Pardalos, P.M.5
Rendl, F.6
-
20
-
-
33845292929
-
Novel formulations for the sequence selection problem in de novo protein design with flexible templates
-
Fung, H. K., M. S. Taylor, and C. A. Floudas. 2007. Novel formulations for the sequence selection problem in de novo protein design with flexible templates. Optim. Methods Software. 22:51-71.
-
(2007)
Optim. Methods Software
, vol.22
, pp. 51-71
-
-
Fung, H.K.1
Taylor, M.S.2
Floudas, C.A.3
-
21
-
-
0141989195
-
Antibacterial activity of synthetic human β-defensin-2 against periodontal bacteria
-
Mineshiba, F., S. Takashiba, J. Mineshiba, K. Matsuura, and S. Kokeguchi. 2003. Antibacterial activity of synthetic human β-defensin-2 against periodontal bacteria. J. Int. Acad. Periodontol. 5:35-40.
-
(2003)
J. Int. Acad. Periodontol
, vol.5
, pp. 35-40
-
-
Mineshiba, F.1
Takashiba, S.2
Mineshiba, J.3
Matsuura, K.4
Kokeguchi, S.5
-
22
-
-
28144451056
-
Human beta-defensin-2 gene transduction of dental pulp cells: A model for pulp antimicrobial gene therapy
-
Huang, G. T., H. B. Zhang, C. Yin, and S. H. Park. 2004. Human beta-defensin-2 gene transduction of dental pulp cells: a model for pulp antimicrobial gene therapy. Int. J. Oral Biol. 29:7-12.
-
(2004)
Int. J. Oral Biol
, vol.29
, pp. 7-12
-
-
Huang, G.T.1
Zhang, H.B.2
Yin, C.3
Park, S.H.4
-
23
-
-
0032693639
-
Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes
-
Matsuzaki, K. 1999. Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes. Biochim. Biophys. Acta. 1462:1-10.
-
(1999)
Biochim. Biophys. Acta
, vol.1462
, pp. 1-10
-
-
Matsuzaki, K.1
-
24
-
-
0032717886
-
Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by α-helical antimicrobial and cell nonselective membrane-lytic peptides
-
Shai, Y. 1999. Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by α-helical antimicrobial and cell nonselective membrane-lytic peptides. Biochim. Biophys. Acta. 1462:55-70.
-
(1999)
Biochim. Biophys. Acta
, vol.1462
, pp. 55-70
-
-
Shai, Y.1
-
25
-
-
0033798839
-
Crystallization of antimicrobial pores in membranes: Magainin and protegrin
-
Yang, L., T. M. Weiss, R. I. Lehrer, and H. W. Huang. 2000. Crystallization of antimicrobial pores in membranes: magainin and protegrin. Biophys. J. 79:2002-2009.
-
(2000)
Biophys. J
, vol.79
, pp. 2002-2009
-
-
Yang, L.1
Weiss, T.M.2
Lehrer, R.I.3
Huang, H.W.4
-
26
-
-
2542480000
-
Multiple Roles of antimicrobial defensins, cathelicidins, and eosinophil-derived neurotoxin in host defense
-
Yang, D., A. Biragyn, D. M. Hoover, J. Lubkowski, and J. J. Oppenheim. 2004. Multiple Roles of antimicrobial defensins, cathelicidins, and eosinophil-derived neurotoxin in host defense. Annu. Rev. Immunol. 22:181-215.
-
(2004)
Annu. Rev. Immunol
, vol.22
, pp. 181-215
-
-
Yang, D.1
Biragyn, A.2
Hoover, D.M.3
Lubkowski, J.4
Oppenheim, J.J.5
-
27
-
-
33745698864
-
Defensins in innate antiviral immunity
-
Klotman, M. E., and T. L. Chang. 2006. Defensins in innate antiviral immunity. Nature Rev. Immunol. 6:447-456.
-
(2006)
Nature Rev. Immunol
, vol.6
, pp. 447-456
-
-
Klotman, M.E.1
Chang, T.L.2
-
28
-
-
9144240994
-
Human epithelial β-defensins 2 and 3 inhibit HIV-1 replication
-
Quiñones Mateu, M. E., M. M. Lederman, Z. Feng, B. Chakraborty, J. Weber, H. R. Rangel, M. L. Marotta, M. Mirza, B. Jiang, P. Kiser, K. Medvik, S. F. Sieg, and A. Weinberg. 2003. Human epithelial β-defensins 2 and 3 inhibit HIV-1 replication. AIDS. 17:F39-F48.
-
(2003)
AIDS
, vol.17
-
-
Quiñones Mateu, M.E.1
Lederman, M.M.2
Feng, Z.3
Chakraborty, B.4
Weber, J.5
Rangel, H.R.6
Marotta, M.L.7
Mirza, M.8
Jiang, B.9
Kiser, P.10
Medvik, K.11
Sieg, S.F.12
Weinberg, A.13
-
29
-
-
27644571478
-
Human β-defensins suppress human immunodeficiency virus infection: Potential role in mucosal protection
-
Sun, L., C. M. Finnegan, T. Kish-Catalone, R. Blumenthal, P. Garzino-Demo, G. M. L. T. Maggiore, S. Berrone, C. Kleinman, Z. Wu, S. Abdelwahab, W. Lu, and A. Garzino-Demo. 2005. Human β-defensins suppress human immunodeficiency virus infection: potential role in mucosal protection. J. Virol. 79:14318-14329.
-
(2005)
J. Virol
, vol.79
, pp. 14318-14329
-
-
Sun, L.1
Finnegan, C.M.2
Kish-Catalone, T.3
Blumenthal, R.4
Garzino-Demo, P.5
Maggiore, G.M.L.T.6
Berrone, S.7
Kleinman, C.8
Wu, Z.9
Abdelwahab, S.10
Lu, W.11
Garzino-Demo, A.12
-
30
-
-
33748744782
-
Mouse salivary glands and human β-defensin-2 as a study model for antimicrobial gene therapy: Technical considerations
-
Yin, C., H. N. Dang, F. Gazor, and G. T.-J. Huang. 2006. Mouse salivary glands and human β-defensin-2 as a study model for antimicrobial gene therapy: technical considerations. Int. J. Antimicrob. Agents. 28:352-360.
-
(2006)
Int. J. Antimicrob. Agents
, vol.28
, pp. 352-360
-
-
Yin, C.1
Dang, H.N.2
Gazor, F.3
Huang, G.T.-J.4
-
31
-
-
85031449537
-
Computational de novo peptide and protein design: Rigid templates versus flexible templates
-
Accepted for publication
-
Fung, H. K., and C. A. Floudas. 2007. Computational de novo peptide and protein design: rigid templates versus flexible templates. Ind. Eng. Chem. Res. Accepted for publication.
-
(2007)
Ind. Eng. Chem. Res
-
-
Fung, H.K.1
Floudas, C.A.2
-
32
-
-
27844505722
-
Advances in protein structure prediction and de novo protein design: A review
-
Floudas, C. A., H. K. Fung, S. R. McAllister, M. Mönnigmann, and R. Rajgaria. 2006. Advances in protein structure prediction and de novo protein design: a review. Chem. Eng. Sci. 61:966-988.
-
(2006)
Chem. Eng. Sci
, vol.61
, pp. 966-988
-
-
Floudas, C.A.1
Fung, H.K.2
McAllister, S.R.3
Mönnigmann, M.4
Rajgaria, R.5
-
33
-
-
0026589733
-
The dead-end elimination theorem and its use in side-chain positioning
-
Desmet, J., M. D. Maeyer, B. Hazes, and I. Lasters. 1992. The dead-end elimination theorem and its use in side-chain positioning. Nature. 356:539-542.
-
(1992)
Nature
, vol.356
, pp. 539-542
-
-
Desmet, J.1
Maeyer, M.D.2
Hazes, B.3
Lasters, I.4
-
34
-
-
0028212927
-
Efficient rotamer elimination applied to protein side-chains and related spin glasses
-
Goldstein, R. 1994. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 66:1335-1340.
-
(1994)
Biophys. J
, vol.66
, pp. 1335-1340
-
-
Goldstein, R.1
-
35
-
-
0001114311
-
Conformational splitting: A more powerful criterion for dead-end elimination
-
Pierce, N., J. Spriet, J. Desmet, and S. Mayo. 2000. Conformational splitting: a more powerful criterion for dead-end elimination. J. Comput. Chem. 21:999-1009.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 999-1009
-
-
Pierce, N.1
Spriet, J.2
Desmet, J.3
Mayo, S.4
-
36
-
-
0034682869
-
Automatic protein design with all atom force-fields by exact and heuristic optimization
-
Wernisch, L., S. Hery, and S. Wodak. 2000. Automatic protein design with all atom force-fields by exact and heuristic optimization. J. Mol. Biol. 301:713-736.
-
(2000)
J. Mol. Biol
, vol.301
, pp. 713-736
-
-
Wernisch, L.1
Hery, S.2
Wodak, S.3
-
37
-
-
0035896029
-
Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
-
Looger, L., and H. Hellinga. 2001. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J. Mol. Biol. 307:429-445.
-
(2001)
J. Mol. Biol
, vol.307
, pp. 429-445
-
-
Looger, L.1
Hellinga, H.2
-
38
-
-
0037472680
-
Exact rotamer optimization for protein design
-
Gordon, B., G. Hom, S. Mayo, and N. Pierce. 2003. Exact rotamer optimization for protein design. J. Comput. Chem. 24:232-243.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 232-243
-
-
Gordon, B.1
Hom, G.2
Mayo, S.3
Pierce, N.4
-
39
-
-
0028343413
-
Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
-
Koehl, P., and M. Delarue. 1994. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:249-275.
-
(1994)
J. Mol. Biol
, vol.239
, pp. 249-275
-
-
Koehl, P.1
Delarue, M.2
-
40
-
-
0034635349
-
Statistical theory of combinatorial libraries of folding proteins: Energetic discrimination of a target structure
-
Zou, J. M., and J. Saven. 2000. Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. J. Mol. Biol. 296:281-294.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 281-294
-
-
Zou, J.M.1
Saven, J.2
-
41
-
-
0035936702
-
Statistical theory of protein combinatorial libraries: Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure
-
Kono, H., and J. Saven. 2001. Statistical theory of protein combinatorial libraries: packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J. Mol. Biol. 306:607-628.
-
(2001)
J. Mol. Biol
, vol.306
, pp. 607-628
-
-
Kono, H.1
Saven, J.2
-
42
-
-
0033550206
-
De novo protein design I. In search of stability and specificity
-
Koehl, P., and M. Levitt. 1999. De novo protein design I. In search of stability and specificity. J. Mol. Biol. 293:1161-1181.
-
(1999)
J. Mol. Biol
, vol.293
, pp. 1161-1181
-
-
Koehl, P.1
Levitt, M.2
-
43
-
-
0041387567
-
A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
-
Dantas, G., B. Kuhlman, D. Callender, M. Wong, and D. Baker. 2003. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332:449-460.
-
(2003)
J. Mol. Biol
, vol.332
, pp. 449-460
-
-
Dantas, G.1
Kuhlman, B.2
Callender, D.3
Wong, M.4
Baker, D.5
-
44
-
-
0037460608
-
Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences
-
Zou, J., and J. Saven. 2003. Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences. J. Chem. Phys. 118:3843-3854.
-
(2003)
J. Chem. Phys
, vol.118
, pp. 3843-3854
-
-
Zou, J.1
Saven, J.2
-
45
-
-
0026179489
-
A new approach to the rapid determination of protein side chain conformations
-
Tuffery, P., C. Etchebest, S. Hazout, and R. Lavery. 1991. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 8:1267-1289.
-
(1991)
J. Biomol. Struct. Dyn
, vol.8
, pp. 1267-1289
-
-
Tuffery, P.1
Etchebest, C.2
Hazout, S.3
Lavery, R.4
-
46
-
-
0030762021
-
Coupling backbone flexibility and amino acid sequence selection in protein design
-
Su, A., and S. Mayo. 1997. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci. 6:1701-1707.
-
(1997)
Protein Sci
, vol.6
, pp. 1701-1707
-
-
Su, A.1
Mayo, S.2
-
47
-
-
0033516509
-
Side chain and backbone flexibility in protein core design
-
Desjarlais, J., and T. Handel. 1999. Side chain and backbone flexibility in protein core design. J. Mol. Biol. 290:305-318.
-
(1999)
J. Mol. Biol
, vol.290
, pp. 305-318
-
-
Desjarlais, J.1
Handel, T.2
-
48
-
-
0033919287
-
Prediction of amino acid sequence from structure
-
Raha, K., A. Wollacott, M. Italia, and J. Desjarlais. 2000. Prediction of amino acid sequence from structure. Protein Sci. 9:1106-1119.
-
(2000)
Protein Sci
, vol.9
, pp. 1106-1119
-
-
Raha, K.1
Wollacott, A.2
Italia, M.3
Desjarlais, J.4
-
49
-
-
0035109198
-
Designed protein G core variants fold to native-like structures: Sequence selection by ORBIT tolerates variation in backbone specification
-
Ross, S., C. Sarisky, A. Su, and S. Mayo. 2001. Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification. Protein Sci. 10:450-454.
-
(2001)
Protein Sci
, vol.10
, pp. 450-454
-
-
Ross, S.1
Sarisky, C.2
Su, A.3
Mayo, S.4
-
50
-
-
0036892389
-
Thoroughly sampling sequence space: Large-scale protein design of structural ensembles
-
Larson, S. M., J. L. England, J. R. Desjarlais, and V. S. Pande. 2002. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci. 11:2804-2813.
-
(2002)
Protein Sci
, vol.11
, pp. 2804-2813
-
-
Larson, S.M.1
England, J.L.2
Desjarlais, J.R.3
Pande, V.S.4
-
51
-
-
0037547120
-
Increased detection of structural templates using alignments of designed sequences
-
Larson, S. M., A. Garg, J. R. Desjarlais, and V. S. Pande. 2003. Increased detection of structural templates using alignments of designed sequences. Proteins. 51:390-396.
-
(2003)
Proteins
, vol.51
, pp. 390-396
-
-
Larson, S.M.1
Garg, A.2
Desjarlais, J.R.3
Pande, V.S.4
-
53
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman, B., G. Dantae, G. Ireton, G. Verani, B. Stoddard, and D. Baker. 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
Dantae, G.2
Ireton, G.3
Verani, G.4
Stoddard, B.5
Baker, D.6
-
54
-
-
12544260150
-
Recapitulation of protein family divergence using flexible backbone protein design
-
Saunders, C. T., and D. Baker. 2005. Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346:631-644.
-
(2005)
J. Mol. Biol
, vol.346
, pp. 631-644
-
-
Saunders, C.T.1
Baker, D.2
-
55
-
-
0029091449
-
Repacking protein cores with backbone freedom: Structure prediction for coiled coils
-
Harbury, P., B. Tidor, T. Alber, and P. Kim. 1995. Repacking protein cores with backbone freedom: structure prediction for coiled coils. Proc. Natl. Acad. Sci. USA. 92:8408-8412.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 8408-8412
-
-
Harbury, P.1
Tidor, B.2
Alber, T.3
Kim, P.4
-
56
-
-
0032553587
-
High-resolution protein design with backbone freedom
-
Harbury, P., J. Plecs, B. Tidor, T. Alber, and P. Kim. 1998. High-resolution protein design with backbone freedom. Science. 282:1462-1467.
-
(1998)
Science
, vol.282
, pp. 1462-1467
-
-
Harbury, P.1
Plecs, J.2
Tidor, B.3
Alber, T.4
Kim, P.5
-
57
-
-
4143120071
-
Structural test of the parameterized-backbone method for protein design
-
Plecs, J., P. B. Harbury, P. Kim, and T. Alber. 2004. Structural test of the parameterized-backbone method for protein design. J. Mol. Biol. 342:289-297.
-
(2004)
J. Mol. Biol
, vol.342
, pp. 289-297
-
-
Plecs, J.1
Harbury, P.B.2
Kim, P.3
Alber, T.4
-
58
-
-
38349081585
-
Overcoming the key challenges in de novo protein design: Enhancing computational efficiency and incorporating true backbone flexibility
-
R. Mondaini, editor. Springer Verlag, Heidelberg
-
Floudas, C. A., H. K. Fung, D. Morikis, M. S. Taylor, and L. Zhang. 2007. Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility. In Modeling of Biosystems: An Interdisciplinary Approach. R. Mondaini, editor. Springer Verlag., Heidelberg.
-
(2007)
Modeling of Biosystems: An Interdisciplinary Approach
-
-
Floudas, C.A.1
Fung, H.K.2
Morikis, D.3
Taylor, M.S.4
Zhang, L.5
-
59
-
-
33750083071
-
Antibacterial activities of synthetic peptides corresponding to the carboxy-terminal region of human β-defensins 1-3
-
Krishnakumari, V., S. Singh, and R. Nagaraj. 2006. Antibacterial activities of synthetic peptides corresponding to the carboxy-terminal region of human β-defensins 1-3. Peptides. 27:2607-2613.
-
(2006)
Peptides
, vol.27
, pp. 2607-2613
-
-
Krishnakumari, V.1
Singh, S.2
Nagaraj, R.3
-
60
-
-
0034693159
-
The structure of human β-defensin-2 shows evidence of higher order oligomerization
-
Hoover, D., K. Rajashankar, R. Blumenthal, A. Puri, J. Oppenheim, O. Chertov, and J. Lubkowski. 2000. The structure of human β-defensin-2 shows evidence of higher order oligomerization. J. Biol. Chem. 275:32911-32918.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 32911-32918
-
-
Hoover, D.1
Rajashankar, K.2
Blumenthal, R.3
Puri, A.4
Oppenheim, J.5
Chertov, O.6
Lubkowski, J.7
-
61
-
-
0037412183
-
Protein design is NP-hard
-
Pierce, N., and E. Winfree. 2002. Protein design is NP-hard. Protein Eng. 15:779-782.
-
(2002)
Protein Eng
, vol.15
, pp. 779-782
-
-
Pierce, N.1
Winfree, E.2
-
62
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
63
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Guntert, P., C. Mumenthaler, and K. Wuthrich. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273:283-298.
-
(1997)
J. Mol. Biol
, vol.273
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wuthrich, K.3
-
64
-
-
4644340524
-
Automated NMR structure calculation with CYANA
-
Guntert, P. 2004. Automated NMR structure calculation with CYANA. J. Mol. Biol. 278:353-378.
-
(2004)
J. Mol. Biol
, vol.278
, pp. 353-378
-
-
Guntert, P.1
-
65
-
-
0346458791
-
A new pairwise folding potential based on improved decoy generation and side chain packing
-
Loose, C., J. Klepeis, and C. Floudas. 2004. A new pairwise folding potential based on improved decoy generation and side chain packing. Proteins Struct. Funct. Bioinformatics. 54:303-314.
-
(2004)
Proteins Struct. Funct. Bioinformatics
, vol.54
, pp. 303-314
-
-
Loose, C.1
Klepeis, J.2
Floudas, C.3
-
66
-
-
0034308163
-
Distance-dependent pair potential for protein folding: Results from linear optimization
-
Tobi, D., and R. Elber. 2000. Distance-dependent pair potential for protein folding: results from linear optimization. Proteins Struct. Funct. Bioinformatics. 41:40-46.
-
(2000)
Proteins Struct. Funct. Bioinformatics
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
67
-
-
0034237798
-
On the design and analysis of protein folding potentials
-
Tobi, D., G. Shafran, N. Linial, and R. Elber. 2000. On the design and analysis of protein folding potentials. Proteins Struct. Funct. Bioinformatics. 40:71-85.
-
(2000)
Proteins Struct. Funct. Bioinformatics
, vol.40
, pp. 71-85
-
-
Tobi, D.1
Shafran, G.2
Linial, N.3
Elber, R.4
-
70
-
-
38349056740
-
Improving the performance of a high resolution distance dependent force field by including protein side chains
-
In press
-
Rajgaria, R., S. R. McAllister, and C. A. Floudas. 2007. Improving the performance of a high resolution distance dependent force field by including protein side chains. Proteins Struct. Funct. Bioinformatics. In press.
-
(2007)
Proteins Struct. Funct. Bioinformatics
-
-
Rajgaria, R.1
McAllister, S.R.2
Floudas, C.A.3
-
71
-
-
25144487283
-
Research challenges, opportunities and synergism in systems engineering and computational biology
-
Floudas, C. A. 2005. Research challenges, opportunities and synergism in systems engineering and computational biology. AIChE J. 51:1872-1884.
-
(2005)
AIChE J
, vol.51
, pp. 1872-1884
-
-
Floudas, C.A.1
-
72
-
-
0000292903
-
Predicting peptide structures using NMR data and deterministic global optimization
-
Klepeis, J. L., C. A. Floudas, D. Morikis, and J. Lambris. 1999. Predicting peptide structures using NMR data and deterministic global optimization. J. Comput. Chem. 20:1354-1370.
-
(1999)
J. Comput. Chem
, vol.20
, pp. 1354-1370
-
-
Klepeis, J.L.1
Floudas, C.A.2
Morikis, D.3
Lambris, J.4
-
73
-
-
0000812896
-
Free energy calculations for peptides via deterministic global optimization
-
Klepeis, J. L., and C. A. Floudas. 1999. Free energy calculations for peptides via deterministic global optimization. J. Chem. Phys. 110:7491-7512.
-
(1999)
J. Chem. Phys
, vol.110
, pp. 7491-7512
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
74
-
-
84867973262
-
Ab initio tertiary structure prediction of proteins
-
Klepeis, J. L., and C. A. Floudas. 2003. Ab initio tertiary structure prediction of proteins. J. Glob. Optim. 25:113-140.
-
(2003)
J. Glob. Optim
, vol.25
, pp. 113-140
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
75
-
-
0037472756
-
Prediction of β-sheet topology and disulfide bridges in polypeptides
-
Klepeis, J. L., and C. A. Floudas. 2003. Prediction of β-sheet topology and disulfide bridges in polypeptides. J. Comput. Chem. 24:191-208.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 191-208
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
76
-
-
84867973262
-
Ab initio tertiary structure prediction of proteins
-
Klepeis, J., and C. Floudas. 2003. Ab initio tertiary structure prediction of proteins. J. Glob. Optim. 25:113-140.
-
(2003)
J. Glob. Optim
, vol.25
, pp. 113-140
-
-
Klepeis, J.1
Floudas, C.2
-
77
-
-
0141642142
-
ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
-
Klepeis, J., and C. Floudas. 2003. ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys. J. 85:2119-2146.
-
(2003)
Biophys. J
, vol.85
, pp. 2119-2146
-
-
Klepeis, J.1
Floudas, C.2
-
78
-
-
1842639266
-
Prediction of oligopeptide conformations via deterministic global optimization
-
Androulakis, I., C. Maranas, and C. A. Floudas. 1997. Prediction of oligopeptide conformations via deterministic global optimization. J. Glob. Optim. 11:1-34.
-
(1997)
J. Glob. Optim
, vol.11
, pp. 1-34
-
-
Androulakis, I.1
Maranas, C.2
Floudas, C.A.3
-
79
-
-
0001327501
-
Alpha BB: A global optimization method for general constrained nonconvex problems
-
Androulakis, I., C. Maranas, and C. A. Floudas. 1995. Alpha BB: a global optimization method for general constrained nonconvex problems. J. Glob. Optim. 7:337-363.
-
(1995)
J. Glob. Optim
, vol.7
, pp. 337-363
-
-
Androulakis, I.1
Maranas, C.2
Floudas, C.A.3
-
80
-
-
0029395174
-
Global optimization for the phase and chemical-equilibrium problem - application to the NRTL equation
-
McDonald, C., and C. Floudas. 1995. Global optimization for the phase and chemical-equilibrium problem - application to the NRTL equation. Comput. Chem. Eng. 19:1111-1139.
-
(1995)
Comput. Chem. Eng
, vol.19
, pp. 1111-1139
-
-
McDonald, C.1
Floudas, C.2
-
81
-
-
34249760465
-
State-of-the-art in global optimization - computational methods and applications - preface
-
Floudas, C., and P. Pardalos. 1995. State-of-the-art in global optimization - computational methods and applications - preface. J. Glob. Optim. 7:113-113.
-
(1995)
J. Glob. Optim
, vol.7
, pp. 113-113
-
-
Floudas, C.1
Pardalos, P.2
-
82
-
-
0029709532
-
A global optimization method, αBB, for process design
-
Suppl. A
-
Adjiman, C., I. Androulakis, C. Maranas, and C. A. Floudas. 1996. A global optimization method, αBB, for process design. Computers Chem. Eng. 20:S419-S424 (Suppl. A.).
-
(1996)
Computers Chem. Eng
, vol.20
-
-
Adjiman, C.1
Androulakis, I.2
Maranas, C.3
Floudas, C.A.4
-
83
-
-
0001466684
-
Global optimization of MINLP problems in process synthesis and design
-
Suppl. S
-
Adjiman, C., I. Androulakis, and C. A. Floudas. 1997. Global optimization of MINLP problems in process synthesis and design. Computers Chem. Eng. 21:S445-S450 (Suppl. S.).
-
(1997)
Computers Chem. Eng
, vol.21
-
-
Adjiman, C.1
Androulakis, I.2
Floudas, C.A.3
-
84
-
-
0030871124
-
Global optimization in generalized geometric programming
-
Maranas, C., and C. A. Floudas. 1997. Global optimization in generalized geometric programming. Computers Chem. Eng. 21:351-369.
-
(1997)
Computers Chem. Eng
, vol.21
, pp. 351-369
-
-
Maranas, C.1
Floudas, C.A.2
-
85
-
-
0032552250
-
A global optimization method, αBB, for general twice-differentiable constrained NPLs. I. Theoretical advances
-
Adjiman, C., I. Androulakis, and C. A. Floudas. 1998. A global optimization method, αBB, for general twice-differentiable constrained NPLs. I. Theoretical advances. Computers Chem. Eng. 22:1137-1158.
-
(1998)
Computers Chem. Eng
, vol.22
, pp. 1137-1158
-
-
Adjiman, C.1
Androulakis, I.2
Floudas, C.A.3
-
86
-
-
0034282316
-
Global optimization of mixed-integer nonlinear problems
-
Adjiman, C., I. Androulakis, and C. A. Floudas. 2000. Global optimization of mixed-integer nonlinear problems. AIChE J. 46:1769-1797.
-
(2000)
AIChE J
, vol.46
, pp. 1769-1797
-
-
Adjiman, C.1
Androulakis, I.2
Floudas, C.A.3
-
87
-
-
0003684555
-
-
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
-
Ponder, J. 1998. TINKER, Software Tools for Molecular Design. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO.
-
(1998)
TINKER, Software Tools for Molecular Design
-
-
Ponder, J.1
-
88
-
-
0001475281
-
Identification of a novel, multifunctional β-defensin (human β-defensin 3) with specific antimicrobial activity
-
García, J., J. Florian, S. Schulz, A. Krause, F. Rodríguez-Jiménez, U. Forssmann, K. Adermann, E. Klüver, C. Vogelmeier, D. Becker, R. Hedrich, W. Forssmann, and R. Bals. 2001. Identification of a novel, multifunctional β-defensin (human β-defensin 3) with specific antimicrobial activity. Cell Tissue Res. 306:257-264.
-
(2001)
Cell Tissue Res
, vol.306
, pp. 257-264
-
-
García, J.1
Florian, J.2
Schulz, S.3
Krause, A.4
Rodríguez-Jiménez, F.5
Forssmann, U.6
Adermann, K.7
Klüver, E.8
Vogelmeier, C.9
Becker, D.10
Hedrich, R.11
Forssmann, W.12
Bals, R.13
-
89
-
-
84986512474
-
CHARMM - a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
90
-
-
84961985307
-
Development of a Generalized Born model parameterization for proteins and nucleic acids
-
Dominy, B., and C. L. Brooks III. 1999. Development of a Generalized Born model parameterization for proteins and nucleic acids. J. Phys. Chem. 103:3765-3773.
-
(1999)
J. Phys. Chem
, vol.103
, pp. 3765-3773
-
-
Dominy, B.1
Brooks III, C.L.2
-
91
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a 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
-
92
-
-
0036667733
-
Knowledge-based potential functions in protein design
-
Russ, W. P., and R. Ranganathan. 2002. Knowledge-based potential functions in protein design. Curr. Opin. Struct. Biol. 12:447-452.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 447-452
-
-
Russ, W.P.1
Ranganathan, R.2
-
93
-
-
0035914442
-
The structure of human β-defensin-1
-
Hoover, D., O. Chertov, and J. Lubkowski. 2001. The structure of human β-defensin-1. J. Biol. Chem. 276:39021-39026.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 39021-39026
-
-
Hoover, D.1
Chertov, O.2
Lubkowski, J.3
-
94
-
-
0000228203
-
A model of evolutionary change in proteins
-
M. O. Dayhoff, editor. National Biomedical Research Foundation, Washington, DC
-
Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure, Vol. 5. M. O. Dayhoff, editor. National Biomedical Research Foundation, Washington, DC.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
95
-
-
0000507749
-
Matrices for detecting distant relationships
-
M. O. Dayhoff, editor. National Biomedical Research Foundation, Washington, DC
-
Schwartz, R. M., and M. O. Dayhoff. 1978. Matrices for detecting distant relationships. In Atlas of Protein Sequence and Structure, Vol. 5. M. O. Dayhoff, editor. National Biomedical Research Foundation, Washington, DC.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
-
-
Schwartz, R.M.1
Dayhoff, M.O.2
|