DOI: 10.1016/s1367-5931(00)00164-2. Protein structure prediction

10.1016/s1367-5931(00)00164-2

Crossref journal-article

Elsevier BV

Current Opinion in Chemical Biology (78)

Bibliography

Al-Lazikani, B., Jung, J., Xiang, Z., & Honig, B. (2001). Protein structure prediction. Current Opinion in Chemical Biology, 5(1), 51â56.

Authors 4

Bissan Al-Lazikani (first)
Joon Jung (additional)
Zhexin Xiang (additional)
Barry Honig (additional)

References 52 Referenced 104

10.1002/(SICI)1097-0134(1999)37:3+<2::AID-PROT2>3.0.CO;2-2 / Proteins / Critical assessment of methods of protein structure prediction (CASP): Round III by Moult (1999)
Lattman EE (Ed): Third Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. Proteins 1999, 37 (suppl 3):1-237. (10.1002/(SICI)1097-0134(1999)37:3+<1::AID-PROT1>3.0.CO;2-6)
10.1146/annurev.biophys.29.1.291 / Annu Rev Biophys Biomol Struct / Comparative protein structure modeling of genes and genomes by Marti-Renom (2000)
10.1093/nar/25.17.3389 / Nucleic Acids Res / Gapped BLAST and psi-blast: a new generation of protein database search programs by Altschul (1997)
10.1006/jmbi.1994.1104 / J Mol Biol / Hidden Markov models in computational biology. Applications to protein modeling by Krogh (1994)
10.1093/bioinformatics/14.10.846 / Bioinformatics / Hidden Markov models for detecting remote protein homologies by Karplus (1998)
Eddy S: HMMer, profile hidden Markov models for biological sequence analysis. On World Wide Web URL: http://hmmer.wustl.edu.
10.1016/S0022-2836(05)80134-2 / J Mol Biol / a structural classification of proteins database for the investigation of sequences and structures by Murzin (1995)
10.1006/jmbi.1999.3233 / J Mol Biol / Benchmarking psi-blast in genome annotation by Müller (1999)
10.1006/jmbi.1999.2653 / J Mol Biol / Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches by Aravind (1999)
10.1006/jmbi.1999.3377 / J Mol Biol / Identification of related proteins on family, superfamily and fold level by Lindahl (2000)
10.1110/ps.9.2.232 / Protein Sci / Comparison of sequence profiles. Strategies for structural predictions using sequence information by Rychlewski (2000)
10.1006/jmbi.2000.3974 / J Mol Biol / An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence by Yang (2000)
10.1006/jmbi.2000.3975 / J Mol Biol / An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments by Yang (2000)
10.1006/jmbi.2000.3741 / J Mol Biol / Enhanced genome annotation using structural profiles in the program 3D-PSSM by Kelley (2000)
10.1006/jmbi.2000.3541 / J Mol Biol / Combination of threading potentials and sequence profiles improves fold recognition by Panchenko (2000)
10.1002/(SICI)1097-0134(1999)37:3+<104::AID-PROT14>3.0.CO;2-P / Proteins / Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure by Jones (1999)
10.1110/ps.9.9.1753 / Protein Sci / Modeling of loops in protein structures by Fiser (2000)
10.1002/(SICI)1097-0134(199602)24:2<209::AID-PROT7>3.0.CO;2-D / Proteins / Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings by Zheng (1996)
10.1002/(SICI)1097-0134(19990501)35:2<173::AID-PROT4>3.0.CO;2-2 / Proteins / Prediction of loop geometries using a Generalized Born model of solvation effects by Rapp (1999)
10.1002/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V / Biopolymers / Protein loops on structurally similar scaffolds: database and conformational analysis by Li (1999)
10.1006/jmbi.1999.2826 / J Mol Biol / New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification by Wojcik (1999)
10.1093/protein/7.8.953 / Protein Eng / Comparison of systematic search and database methods for constructing segments of protein structure by Fidelis (1994)
10.1006/jmbi.1996.0857 / J Mol Biol / PDB-based protein loop prediction: parameters for selection and methods for optimization by Vlijmen (1997)
10.1002/prot.340180205 / Proteins / Evaluation of the conformational free energies of loops in proteins by Smith (1994)
10.1002/(SICI)1097-0134(19991001)37:1<56::AID-PROT6>3.0.CO;2-7 / Proteins / Importance of anchor group positioning in protein loop prediction by Lessel (1999)
10.1016/0022-2836(87)90358-5 / J Mol Biol / Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequence for different structure classes by Ponder (1987)
10.1006/jmbi.1993.1170 / J Mol Biol / Backbone-dependent rotamer library for proteins. Application to side-chain prediction by Dunbrack (1993)
10.1016/S1359-0278(97)00006-0 / Fold Des / All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination by Maeyer (1997)
10.1016/0301-4622(94)00047-6 / Biophys Chem / Relation between volume correction and the standard state by Lee (1994)
10.1016/0022-2836(91)90550-P / J Mol Biol / Prediction of protein side-chain conformation by packing optimization by Lee (1991)
10.1073/pnas.94.19.10172 / Proc Natl Acad Sci USA / Probing the role of packing specificity in protein design by Dahiyat (1997)
10.1016/S0969-2126(99)80176-2 / Structure Fold Des / Branch-and-terminate: a combinatorial optimization algorithm for protein design by Gordon (1999)
10.1016/S0959-440X(96)80077-7 / Curr Opin Struct Biol / Modeling side-chain conformation by Vasquez (1996)
10.1006/jmbi.1997.0926 / J Mol Biol / Homology modeling with a backbone-dependent rotamer library by Bower (1997)
10.1006/jmbi.1994.1366 / J Mol Biol / Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy by Koelh (1994)
10.1093/protein/11.11.991 / Protein Eng / Determinants of side chain conformational preferences in protein structures by Samudrala (1998)
10.1002/(SICI)1097-0282(199908)50:2<111::AID-BIP1>3.0.CO;2-N / Biopolymers / Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction by Mendes (1999)
10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2 / Proteins / The penultimate rotamer library by Lovell (2000)
10.1002/(SICI)1097-0134(19981101)33:2<204::AID-PROT5>3.0.CO;2-I / Proteins / Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods by Huang (1998)
10.1016/S0959-440X(00)00063-4 / Curr Opin Struct Biol / Effective energy functions for protein structure prediction by Lazaridis (2000)
10.1006/jmbi.1997.1479 / J Mol Biol / An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction by Samudrala (1998)
10.1016/0959-440X(95)80081-6 / Curr Opin Struct Biol / Knowledge-based potentials for proteins by Sippl (1995)
10.1002/pro.5560070812 / Protein Sci / Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms by Janardhan (1998)
10.1002/(SICI)1097-0134(19980901)32:4<399::AID-PROT1>3.0.CO;2-C / Proteins / Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model by Vorobjev (1998)
10.1006/jmbi.1999.2685 / J Mol Biol / Discrimination of the native from misfolded protein models with an energy function including implicit solvation by Lazaridis (1999)
Petrey D, Honig B: Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci 2000, in press.charmm22 force field and a Poisson-Boltzmann solvation model are used to distinguish native structures. It is shown that the Coulomb energy generally favors the native conformation and, on this basis, a simplified scoring function is developed. (10.1110/ps.9.11.2181)
10.1002/(SICI)1097-0134(1999)37:3+<204::AID-PROT26>3.0.CO;2-F / Proteins / Calculation of protein conformation by global optimization of a potential energy function by Lee (1999)
10.1021/ja00172a038 / J Am Chem Soc / Semi-analytical treatment of solvation for molecular mechanics and dynamics by Still (1990)
10.1006/jmbi.1995.0529 / J Mol Biol / Recognizing native folds by the arrangement of hydrophobic an polar residues by Huang (1995)
10.1016/S0923-2508(00)00121-2 / Res Microbiol. / Protein structure computing in the genomic era by Schwede (2000)
10.1093/nar/28.1.250 / Nucleic Acids Res / MODBASE, a database of annotated comparative protein structure models by Sanchez (2000)

Dates

Type	When
Created	23 years, 1 month ago (July 25, 2002, 3:46 p.m.)
Deposited	6 years, 4 months ago (April 22, 2019, 4:21 a.m.)
Indexed	3 weeks, 2 days ago (Aug. 6, 2025, 8:38 a.m.)
Issued	24 years, 6 months ago (Feb. 1, 2001)
Published	24 years, 6 months ago (Feb. 1, 2001)
Published Print	24 years, 6 months ago (Feb. 1, 2001)

Funders 0

None

BibTeX

@article{Al_Lazikani_2001, title={Protein structure prediction}, volume={5}, ISSN={1367-5931}, url={http://dx.doi.org/10.1016/s1367-5931(00)00164-2}, DOI={10.1016/s1367-5931(00)00164-2}, number={1}, journal={Current Opinion in Chemical Biology}, publisher={Elsevier BV}, author={Al-Lazikani, Bissan and Jung, Joon and Xiang, Zhexin and Honig, Barry}, year={2001}, month=feb, pages={51–56} }

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      "author": "Lee",
      "year": "1994",
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      "volume": "217",
      "author": "Lee",
      "year": "1991",
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      "author": "Dahiyat",
      "year": "1997",
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      "author": "Gordon",
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      "author": "Vasquez",
      "year": "1996",
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      "author": "Bower",
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      "volume": "239",
      "author": "Koelh",
      "year": "1994",
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      "author": "Samudrala",
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      "author": "Mendes",
      "year": "1999",
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      "author": "Lovell",
      "year": "2000",
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      "author": "Huang",
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      "author": "Lazaridis",
      "year": "2000",
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      "year": "1998",
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      "author": "Sippl",
      "year": "1995",
      "journal-title": "Curr Opin Struct Biol"
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    {
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      "author": "Janardhan",
      "year": "1998",
      "journal-title": "Protein Sci"
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      "volume": "32",
      "author": "Vorobjev",
      "year": "1998",
      "journal-title": "Proteins"
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      "volume": "288",
      "author": "Lazaridis",
      "year": "1999",
      "journal-title": "J Mol Biol"
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      "unstructured": "Petrey D, Honig B: Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci 2000, in press.charmm22 force field and a Poisson-Boltzmann solvation model are used to distinguish native structures. It is shown that the Coulomb energy generally favors the native conformation and, on this basis, a simplified scoring function is developed.",
      "DOI": "10.1110/ps.9.11.2181"
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      "volume": "37",
      "author": "Lee",
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      "article-title": "Semi-analytical treatment of solvation for molecular mechanics and dynamics",
      "volume": "112",
      "author": "Still",
      "year": "1990",
      "journal-title": "J Am Chem Soc"
    },
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      "author": "Huang",
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      "article-title": "Protein structure computing in the genomic era",
      "volume": "151",
      "author": "Schwede",
      "year": "2000",
      "journal-title": "Res Microbiol."
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      "author": "Sanchez",
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