Protein structure prediction

Current Opinion in Chemical Biology

Volumn 5, Issue 1, 2001, Pages 51-56

  Al Lazikani, Bissan ^a   Jung, Joon ^a   Xiang, Zhexin ^a   Honig, Barry ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY;

EID: 0035252674     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(00)00164-2     Document Type: Review

References (52)

1. Critical assessment of methods of protein structure prediction (CASP): Round III
2. Third Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
3. Comparative protein structure modeling of genes and genomes
4. Gapped BLAST and psi-blast: A new generation of protein database search programs
5. Hidden Markov models in computational biology. Applications to protein modeling
6. Hidden Markov models for detecting remote protein homologies
7. SCOP: A structural classification of proteins database for the investigation of sequences and structures
8. Benchmarking psi-blast in genome annotation
9. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
10. Identification of related proteins on family, superfamily and fold level
11. Comparison of sequence profiles. Strategies for structural predictions using sequence information
12. 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
13. 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
14. Enhanced genome annotation using structural profiles in the program 3D-PSSM
15. Combination of threading potentials and sequence profiles improves fold recognition
16. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
17. Modeling of loops in protein structures
18. Accuracy and reliability of the scaling-relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational samplings
19. Prediction of loop geometries using a Generalized Born model of solvation effects
20. Protein loops on structurally similar scaffolds: Database and conformational analysis
21. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification
22. Comparison of systematic search and database methods for constructing segments of protein structure
23. PDB-based protein loop prediction: Parameters for selection and methods for optimization
24. Evaluation of the conformational free energies of loops in proteins
25. Importance of anchor group positioning in protein loop prediction
26. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequence for different structure classes
27. Backbone-dependent rotamer library for proteins. Application to side-chain prediction
28. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination
29. Relation between volume correction and the standard state
30. Prediction of protein side-chain conformation by packing optimization
31. Probing the role of packing specificity in protein design
32. Branch-and-terminate: A combinatorial optimization algorithm for protein design
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34. Homology modeling with a backbone-dependent rotamer library
35. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
36. Determinants of side chain conformational preferences in protein structures
37. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction
38. The penultimate rotamer library
39. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
40. Effective energy functions for protein structure prediction
41. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
42. Knowledge-based potentials for proteins
43. Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms
44. 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
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48. Semi-analytical treatment of solvation for molecular mechanics and dynamics
49. Recognizing native folds by the arrangement of hydrophobic an polar residues
50. Protein structure computing in the genomic era
51. MODBASE, a database of annotated comparative protein structure models