Continuum secondary structure captures protein flexibility

Structure

Volumn 10, Issue 2, 2002, Pages 175-184

  Andersen, Claus A F ^a,b   Palmer, Arthur G ^a   Brunak, Soren ^b   Rost, Burkhard ^a  

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

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Evaluation; NMR spectroscopy; Protein function; Protein motion; Protein secondary structure assignment; Protein structure prediction; Structure comparison

Indexed keywords

ARTICLE; HYDROGEN BOND; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY;

COMPUTER SYSTEMS; HYDROGEN BONDING; INTERNET; MODELS, MOLECULAR; MOTION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PLIABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0036174712     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00700-1     Document Type: Article

References (59)

1. The Protein Data Bank
2. Two hydrogen-bonded helical configurations of the polypeptide chain
3. Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
4. How good are predictions of protein secondary structure?
5. Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure
6. Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis
7. Conformation of polypeptides and proteins
8. Knowledge-based protein secondary structure assignment
9. Amino acid preference for specific locations at the end of α helices
10. Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
11. New approaches to study macromolecular structure and function
12. Unveiling ribosomal structures: The final phases
13. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex
14. Backbone dynamics of calmodulin studied by nitrogen-15 relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
15. Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant
16. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?
17. Molecular dynamics and accuracy of NMR structures: Effects of error bounds and data removal
18. NMR probes of molecular dynamics: Overview and comparison with other techniques
19. Helix stop signals in proteins and peptides: The capping box
20. Helix capping
21. β-breakers: An aperiodic secondary structure
22. Non-linearities in training sets identified by inspecting the order in which neural networks learn
23. Protein structure and the sequential structure of mRNA: α-helix and β-sheet signals at the nucleotide level
24. Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments
25. 1D secondary structure prediction through evolutionary profiles
26. Helmholtz free energy of peptide hydrogen bonds in proteins
27. Prediction of protein secondary structure at 80% accuracy
28. Protein secondary structure prediction continues to rise
29. Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F
30. Are proteins even floppier than we thought?
31. A protein taxonomy based on secondary structure
32. TOPITS: Threading one-dimensional predictions into three-dimensional structures
33. Predicting conformational switches in proteins
34. Touring protein fold space with Dali/FSSP
35. Steriochemical quality of protein structure coordinates
36. AQUA and PROCHECH-NMR: Programs for checking the quality of protein structures solved by NMR
37. What if: A molecular modeling and drug design program
38. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation
39. Conformational variability of solution nuclear magnetic resonance structures
40. Defining the precision with which a protein structure is determined by NMR. Application to motolin
41. Completeness of NOEs in protein structures: A statistical analysis of NMR data
42. Quality assessment of NMR structures: A statistical survey
43. Validation of nuclear magnetic resonance structures of proteins and nucleic acids: Hydrogen geometry and nomenclature
44. Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1
45. 2 binding pathway
46. Solution structure and dynamics of the DNA-binding domain of the adipocyte-transcription factor FREAC-11
47. The three-dimensional solution structure and dynamic properties of the human FADD death domain
48. High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: Implications for phosphorylation and molecular recognition
49. Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO
50. High-resolution solution structures of oxidized and reduced Escherichia coli thioredoxin
51. Calculations of NMR dipolar coupling strengths in model peptides
52. Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters
53. A relational database for sequence-specific protein NMR data
54. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
55. MOLMOL: A program for display and analysis of macromolecular structures
56. Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
57. A new class of hexahelical insect proteins revealed as putative carriers of small hydrophobic ligands