DOI: 10.1016/s1359-0278(98)00064-9. Packing of sidechains in low-resolution models for proteins

Packing of sidechains in low-resolution models for proteins

10.1016/s1359-0278(98)00064-9

Crossref journal-article

Elsevier BV

Folding and Design (78)

Bibliography

Keskin, O., & Bahar, I. (1998). Packing of sidechains in low-resolution models for proteins. Folding and Design, 3(6), 469â479.

Authors 2

Ozlem Keskin (first)
Ivet Bahar (additional)

References 36 Referenced 17

10.1002/bip.360360106 / Biopolymers / An evaluation of discrete and continuum search techniques for conformational analysis of sidechains in proteins by Vasquez (1995)
10.1016/0022-2836(91)90550-P / J. Mol. Biol / Prediction of side-chain conformation by packing optimization by Lee (1991)
10.1002/(SICI)1097-0134(199611)26:3<323::AID-PROT8>3.0.CO;2-E / Proteins / Prediction and evaluation of side-chain conformations for protein backbone structures by Shenkin (1996)
10.1146/annurev.biochem.66.1.549 / Annu. Rev. Biochem / Protein folding: the endgame by Levitt (1997)
10.1016/0022-2836(90)90086-2 / J. Mol. Biol / Novel method for the rapid evaluation of packing in protein structures by Gregoret (1990)
10.1006/jmbi.1993.1331 / J. Mol. Biol / A method to configure protein side-chains from the main-chain trace in homology modelling by Eisenmenger (1993)
10.1002/(SICI)1096-987X(19961115)17:14<1667::AID-JCC8>3.0.CO;2-J / J Comp. Chem / A new method for sidechain conformation prediction using a Hopfield network and reproduced rotamers by Kono (1996)
10.1080/07391102.1991.10507882 / J. Biomol. Struct. Dynam / A new approach to the rapid determination of protein sidechain conformations by Tuffery (1991)
10.1002/pro.5560040619 / Protein Sci / Building proteins from Cα coordinates using the dihedral probability grid Monte Carlo method by Mathiowetz (1995)
10.1016/0022-2836(91)90883-8 / J. Mol. Biol / Database algorithm for generating protein backbone and sidechain coordinates from a Cα trace by Holm (1991)
10.1002/jcc.540130407 / J. Comp. Chem / Efficient algorithm for the reconstruction of a protein backbone from the α-carbon coordinates by Rey (1992)
10.1002/(SICI)1097-0134(199711)29:3<370::AID-PROT10>3.0.CO;2-K / Proteins / Non-randomness in side-chain packing: the distribution of interplanar angles by Mitchell (1997)
10.1016/0022-2836(87)90358-5 / J. Mol. Biol / Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes by Ponder (1987)
10.1002/pro.5560060807 / Protein Sci / Bayesian statistical analysis of protein side-chain rotamer preferences by Dunbrack (1997)
10.1016/0022-2836(92)90964-L / J. Mol. Biol / Accurate modeling of protein conformation by automatic segment matching by Levitt (1992)
10.1006/jmbi.1994.1366 / J. Mol. Biol / Application of a self-consistent mean field theory to predict protein sidechains conformation and estimate their conformational entropy by Koehl (1994)
10.1006/jmbi.1994.1059 / J. Mol. Biol / Prediction of protein side-chain conformations from local three-dimensional homology relationships by Laughton (1994)
10.1006/jmbi.1993.1100 / J. Mol. Biol / Modelling side-chain conformation for homologous proteins using an energy-based rotamer search by Wilson (1993)
10.1016/0022-2836(87)90520-1 / J. Mol. Biol / Analysis of side-chain orientations in homologous proteins by Summers (1987)
10.1006/jmbi.1993.1170 / J. Mol. Biol / Backbone-dependent rotamer library for proteins, application to sidechain prediction by Dunbrack (1993)
10.1016/0959-440X(92)90154-Y / Curr. Opin. Struct. Biol / Protein folds by Jernigan (1992)
10.1006/jmbi.1995.0311 / J. Mol. Biol / The complexity and accuracy of discrete state models of protein structure by Park (1995)
10.1038/253694a0 / Nature / Computer simulation of protein folding by Levitt (1975)
10.1073/pnas.88.10.4195 / Proc. Natl Acad. Sci. USA / The protein folding problem: the native fold determines packing, but does packing determines the native fold? by Behe (1991)
10.1002/pro.5560030702 / Protein Sci / Sidechain entropy and packing in proteins by Bromberg (1994)
10.1073/pnas.92.18.8408 / Proc. Natl Acad. Sci. USA / Repacking protein cores with backbone freedom: Structure prediction for coiled coils by Harbury (1995)
10.1002/pro.5560061003 / Protein Sci / Ideal architecture of residue packing and its observation in protein structures by Raghunathan (1997)
10.1126/science.8259514 / Science / The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme by Baldwin (1993)
10.1016/S1359-0278(96)00051-X / Fold. Des / Coordination geometry of nonbonded residues in globular proteins by Bahar (1996)
10.1006/jmbi.1996.0758 / J. Mol. Biol / Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation by Bahar (1997)
10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D / Proteins / Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches by Bahar (1997)
10.1016/S0959-440X(96)80075-3 / Curr. Opin. Struct. Biol / Structure-derived potentials and protein simulations by Jernigan (1996)
{'key': '10.1016/S1359-0278(98)00064-9_bib33', 'series-title': 'Crystallographic Databases-Information Content Software Systems, Scientific Applications', 'first-page': '107', 'author': 'Abola', 'year': '1987'} / Crystallographic Databases-Information Content Software Systems, Scientific Applications by Abola (1987)
10.1002/pro.5560030922 / Protein Sci / Pseudodihedrals: simplified protein backbone representation with knowledge-based energy by DeWitte (1994)
10.1006/jmbi.1996.0256 / J. Mol. Biol / Energy functions that discriminate X-ray and near-native folds from well-constructed decoys by Park (1996)
10.1021/ma00145a039 / Macromolecules / Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation by Miyazawa (1985)

Dates

Type	When
Created	20 years, 1 month ago (July 12, 2005, 5:55 p.m.)
Deposited	6 years, 7 months ago (Jan. 24, 2019, 10:52 a.m.)
Indexed	1 year, 6 months ago (Feb. 11, 2024, 5:58 a.m.)
Issued	26 years, 9 months ago (Nov. 1, 1998)
Published	26 years, 9 months ago (Nov. 1, 1998)
Published Print	26 years, 9 months ago (Nov. 1, 1998)

Funders 0

None

BibTeX

@article{Keskin_1998, title={Packing of sidechains in low-resolution models for proteins}, volume={3}, ISSN={1359-0278}, url={http://dx.doi.org/10.1016/s1359-0278(98)00064-9}, DOI={10.1016/s1359-0278(98)00064-9}, number={6}, journal={Folding and Design}, publisher={Elsevier BV}, author={Keskin, Ozlem and Bahar, Ivet}, year={1998}, month=nov, pages={469–479} }

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