Evaluation of comparative protein modeling by MODELLER

Proteins: Structure, Function, and Bioinformatics

Volumn 23, Issue 3, 1995, Pages 318-326

  Šali, Andrej ^a,c   Potterton, Liz ^b   Yuan, Feng ^c   van Vlijmen, Herman ^c   Karplus, Martin ^c  

^a ROCKEFELLER UNIVERSITY   (United States)

^b UNIVERSITY OF YORK   (United Kingdom)

^c HARVARD UNIVERSITY   (United States)

Author keywords

comparative protein modeling; evaluation

Indexed keywords

NEUROTOXIN; NUCLEOSIDE DIPHOSPHATE KINASE; RETINOIC ACID BINDING PROTEIN;

ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; EOSINOPHIL; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMAL; COMPUTER COMMUNICATION NETWORKS; COMPUTER GRAPHICS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; HUMAN; MAGNETIC RESONANCE SPECTROSCOPY; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUROTOXINS; NUCLEOSIDE-DIPHOSPHATE KINASE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, RETINOIC ACID; SEQUENCE ALIGNMENT; SOFTWARE; SUPPORT, U.S. GOV'T, NON-P.H.S.; TEMPLATES, GENETIC;

EID: 0028871814     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.340230306     Document Type: Article

References (39)

1. Crystal structure of cellular retinoic acid‐binding proteins I and II in complex with all trans‐retinoic acid and a synthetic retinoid
2. From comparisons of protein sequences and structures to protein modelling and design
3. Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
4. Comparative protein modelling by satisfaction of spatial restraints
5. Derivation of rules for comparative protein modeling from a database of protein structure alignments
6. Comparative protein modelling by satisfaction of spatial restraints
7. Protein Data Bank
8. Three‐dimensional models of four mouse mast cell chymases. Identification of proteoglycan‐binding regions and protease specific antigenic epitopes
9. Modeling mutations and homologous proteins
10. Knowledge‐based protein modelling
11. Knowledge‐based model building of proteins: Concepts and examples
12. Confidence limits on phylogenies: An approach using the bootstrap
13. A general method applicable to the search for similarities in the amino acid sequence of two proteins
14. Knowledge based modelling of homologous proteins, Part I: Three dimensional frameworks derived from the simultaneous superposition of multiple structures
15. CHARMM: A program for macromolecular energy minimization and dynamics calculations
16. PROCHECK: A program to check the stereochemical quality of protein structures
17. Recognition of errors in three‐dimensional structures of proteins
18. Assessment of protein models with three‐dimensional profiles
19. Modeling of globular proteins: a distance‐based search procedure for the construction of insertion/deletion regions and Pro α non‐Pro mutations
20. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
21. Prediction of protein sidechain conformations from a backbone conformation dependent rotamer library
22. Tertiary structural constraints on protein evolutionary diversity; templates, key residues and structure prediction
23. An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure
24. Molecular dynamics of native protein. II. Analysis and nature of motion
25. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
26. Comparison of systematic search and database methods for constructing segments of protein structure
27. Analysis of two‐residue turns in proteins
28. The crystal structure of an engineered monomeric triosephosphate isomerase, monoTim: The correct modelling of an eight residue loop
29. A structural basis for sequence comparisons: An evaluation of scoring methodologies
30. A new approach to protein fold recognition
31. Topology fingerprint approach to the inverse protein folding problem
32. Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1β
33. Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy
34. An assessment of the precision and accuracy of protein structures determined by NMR
35. A mutant T4 lysozyme displays five different crystal conformations
36. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
37. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure
38. Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines in mouse mast cell protease‐7 regulates its binding to heparin serglycin proteoglycan