Crossref journal-article
Elsevier BV
Journal of Molecular Biology (78)
Bibliography

Lazaridis, T., & Karplus, M. (1999). Discrimination of the native from misfolded protein models with an energy function including implicit solvation. Journal of Molecular Biology, 288(3), 477–487.

Authors 2
  1. Themis Lazaridis (first)
  2. Martin Karplus (additional)
References 46 Referenced 225
  1. 10.1002/(SICI)1096-987X(199610)17:13<1549::AID-JCC6>3.0.CO;2-S / J. Comp. Chem / An efficient, differentiable hydration potential of peptides and proteins by Augspurger (1996)
  2. 10.1002/(SICI)1096-987X(199706)18:8<1072::AID-JCC11>3.0.CO;2-F / J. Comp. Chem / An assessment of the accuracy of the RRIGS hydration potential by Augspurger (1997)
  3. 10.1126/science.1853201 / Science / A method to identify protein sequences that fold into a known three-dimensional structure by Bowie (1991)
  4. 10.1002/jcc.540040211 / J. Comput. Chem / CHARMM by Brooks (1983)
  5. 10.1002/9780470141205.ch1 / Advan. Chem. Phys / Proteins by Brooks (1988)
  6. 10.1073/pnas.84.21.7524 / Proc. Natl Acad. Sci. USA / Spin glasses and the statistical mechanics of protein folding by Bryngelson (1987)
  7. 10.1016/0022-2836(92)90556-Y / J. Mol. Biol / Structure-derived hydrophobic potential by Casari (1992)
  8. 10.1002/pro.5560070314 / Protein Sci / Locally accessible conformations of proteins by Caves (1998)
  9. 10.1093/protein/9.8.637 / Protein Eng / Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures by DeBolt (1996)
  10. 10.1038/319199a0 / Nature / Solvation energy in protein folding and binding by Eisenberg (1986)
  11. 10.1126/science.3798113 / Science / Multiple conformational states of proteins by Elber (1987)
  12. 10.1016/S0959-440X(97)80008-5 / Curr. Opin. Struct. Biol / Protein structure by Finkelstein (1997)
  13. 10.1006/jmbi.1996.0139 / J. Mol. Biol / An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution by Fraternali (1996)
  14. 10.1126/science.1749933 / Science / The energy landscapes and motions of proteins by Frauenfelder (1991)
  15. {'key': '10.1006/jmbi.1999.2685_BIB15', 'first-page': '109', 'article-title': 'Minimization of polypeptide energy V. Theoretical aspects', 'volume': '1', 'author': 'Gibson', 'year': '1969', 'journal-title': 'Physiol. Chem. Phys'} / Physiol. Chem. Phys / Minimization of polypeptide energy V. Theoretical aspects by Gibson (1969)
  16. 10.1016/0022-2836(92)91028-N / J. Mol. Biol / Evaluation of protein models by atomic solvation preference by Holm (1992)
  17. 10.1021/j100026a035 / J. Phys. Chem / Simulated annealing of a protein in a continuum solvation by multiple-time-step molecular dynamics by Humphreys (1995)
  18. 10.1021/j100299a032 / J. Chem. Phys / Free energies of hydration of solute molecules 1. Improvement of the hydration shell model by exact computations of overlap volumes by Kang (1987)
  19. {'key': '10.1006/jmbi.1999.2685_BIB19', 'first-page': '127', 'article-title': 'Protein folding', 'author': 'Karplus', 'year': '1992'} / Protein folding by Karplus (1992)
  20. 10.1016/S0006-3495(87)83303-9 / Biophys. J / Configurational entropy of native proteins by Karplus (1987)
  21. 10.1002/prot.340200307 / Proteins: Struct. Funct. Genet / Polar and nonpolar environments in the protein core by Koehl (1994)
  22. 10.1126/science.278.5345.1928 / Science / “New view” of protein folding reconciled with the old through multiple unfolding simulations by Lazaridis (1997)
  23. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N / Proteins: Struct. Funct. Genet / Effective energy function for proteins in solution by Lazaridis (1999)
  24. 10.1016/S0022-2836(83)80306-4 / J. Mol. Biol / Molecular dynamics of native protein II. Analysis and nature of motion by Levitt (1983)
  25. 10.1002/(SICI)1097-0134(1997)1+<83::AID-PROT12>3.0.CO;2-N / Proteins: Struct. Funct. Genet / A retrospective analysis of CASP2 threading predictions by Marchler-Bauer (1997)
  26. 10.1006/jmbi.1998.2071 / J. Mol. Biol / Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulphide bond constraints by Marti-Renom (1998)
  27. 10.1006/jmbi.1995.0195 / J. Mol. Biol / Computer modeling of protein folding by Monge (1995)
  28. 10.1016/S0959-440X(97)80025-5 / Curr. Opin. Struct. Biol / Comparison of database potential and molecular mechanics force fields by Moult (1997)
  29. 10.1063/1.472061 / J. Chem. Phys / Simulation of activation free energies in molecular systems by Neria (1996)
  30. 10.1002/prot.340050203 / Proteins: Struct. Funct. Genet / Structural basis of hierarchical multiple substates of a protein. I. Introduction by Noguti (1989)
  31. 10.1016/0022-2836(84)90049-4 / J. Mol. Biol / An analysis of incorrectly folded protein models. Implications for structure predictions by Novotny (1984)
  32. 10.1002/prot.340040105 / Proteins: Struct. Funct. Genet / Criteria that discriminate between native proteins and incorrectly folded models by Novotny (1988)
  33. 10.1006/jmbi.1996.0256 / J. Mol. Biol / Energy functions that discriminate X-ray and near-native fold from well-constructed decoys by Park (1996)
  34. 10.1006/jmbi.1996.0809 / J. Mol. Biol / Factors affecting the ability of energy functions to discriminate correct from incorrect folds by Park (1997)
  35. 10.1006/jmbi.1993.1417 / J. Mol. Biol / Contribution of hydration to protein folding thermodynamics II. The entropy and Gibbs energy of hydration by Privalov (1993)
  36. 10.1093/protein/10.8.865 / Protein Eng / Residue-residue mean-force potentials for protein structure recognition by Reva (1997)
  37. 10.1038/369248a0 / Nature / How does a protein fold? by Šali (1994)
  38. 10.1006/jmbi.1997.1479 / J. Mol. Biol / An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction by Samudrala (1998)
  39. 10.1038/nsb0594-301 / Nature Struct. Biol / Comparison of 4 independently determined structures of human recombinant interleukin-4 by Smith (1994)
  40. 10.1021/ja00172a038 / J. Am. Chem. Soc / Semianalytical treatment of solvation for molecular mechanics and dynamics by Still (1990)
  41. 10.1080/08927029308022161 / Mol. Simul / An effective solvation term based on atomic occupancies for use in protein simulations by Stouten (1993)
  42. {'key': '10.1006/jmbi.1999.2685_BIB42', 'series-title': 'GROMOS', 'author': 'van Gunsteren', 'year': '1987'} / GROMOS by van Gunsteren (1987)
  43. 10.1002/(SICI)1097-0134(19980901)32:4<399::AID-PROT1>3.0.CO;2-C / Proteins: Struct. Funct. Genet / Discrimination between native and intentionally misfolded conformations of proteins by Vorobjev (1998)
  44. 10.1073/pnas.92.3.709 / Proc. Natl Acad. Sci. USA / Discriminating compact nonnative structures from the native structure of globular proteins by Wang (1995)
  45. 10.1002/pro.5560010204 / Protein Sci / Atomic solvation parameters applied to molecular dynamics of proteins in solution by Wesson (1992)
  46. 10.1002/prot.340140112 / Proteins: Struct. Funct. Genet / Empirical solvation models in the context of conformational energy searches by Williams (1992)
Dates
Type When
Created 22 years, 10 months ago (Oct. 7, 2002, 7:22 a.m.)
Deposited 6 years, 3 months ago (May 6, 2019, 8:26 p.m.)
Indexed 3 weeks, 6 days ago (July 30, 2025, 9:58 a.m.)
Issued 26 years, 3 months ago (May 1, 1999)
Published 26 years, 3 months ago (May 1, 1999)
Published Print 26 years, 3 months ago (May 1, 1999)
Funders 0

None

@article{Lazaridis_1999, title={Discrimination of the native from misfolded protein models with an energy function including implicit solvation}, volume={288}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.1999.2685}, DOI={10.1006/jmbi.1999.2685}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Lazaridis, Themis and Karplus, Martin}, year={1999}, month=may, pages={477–487} }