Modeling the anti‐CEA antibody combining site by homology and conformational search

Proteins: Structure, Function, and Bioinformatics

Volumn 14, Issue 4, 1992, Pages 483-498

  Mas, Maria T ^a   Smith, Kenneth C ^b   Yarmush, David L ^b   Aisaka, Kazuo ^a,d   Fine, Richard M ^b,c  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

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

^c Biosym Technologies Inc   (United States)

^d KYOWA HAKKO KOGYO CO LTD   (Japan)

Author keywords

antibody; canonical structures; CDR; CEA; conformational search; homology modeling; rotamers; tweak

Indexed keywords

ANTIBODY; CARCINOEMBRYONIC ANTIGEN;

ANTIBODY COMBINING SITE; ANTIGEN BINDING; ARTICLE; CALCULATION; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANTIBODIES; BINDING SITES, ANTIBODY; CARCINOEMBRYONIC ANTIGEN; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, NON-P.H.S.; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0026492031     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.340140409     Document Type: Article

References (61)

1. Three‐dimensional structure of antibodies
2. Antibody‐antigen complexes
3. The three‐dimensional structure of a combining region ligand complex of immunoglobulin NEW at 3.5 Å resolution
4. Binding of 2,4‐dinitrophenyl compounds and other small molecules to a crystalline λ‐type Bence‐Jones dimer
5. The three dimensional structure of a phosphocholine‐binding mouse immunoglobulin Fab and the nature of the antigen binding site
6. The molecular structure of a dimer composed of the variable portions of the Bence Jones protein Rei refined at 2.0 Å resolution
7. Preliminary refinement and structural analysis of the Fab fragment from the human immunoglobulin New at 2.0 Å
8. Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen‐binding fragment at 3.0 Å and 1.9 Å resolution
9. Structure of a novel Bence‐Jones protein (Rhe) fragment at 1.6 Å resolution
10. Three‐dimensional structure of an antigen‐antibody complex at 2.8 Å resolution
11. Phosphocholine binding immunoglobulin Fab McPC603. An X‐ray diffraction study at 2.7 Angstroms
12. The galactan‐binding immunoglobulin Fab J 539: An x‐ray diffraction study at 2.6 Å resolution
13. Three‐dimensional structure of a complex of antibody with influenza virus neuraminidase
14. Three‐dimensional structure of an antibody‐antigen complex: Proc Natl
15. Three‐dimensional structure of a fluorescein‐fab complex crystallized in 2‐methyl‐2,4‐pentanediol
16. Structure of an antibody‐antigen complex: Crystal structure of the HyHEL‐10 Fablysozyme complex
17. Three‐dimensional structure of murine anti‐p‐azophenylarsonate Fab 36–71. I. X‐ray crystallography, site‐directed mutagenesis, and modeling of the complex with hapten
18. Monoclonal antibodies for carcinoembryonic antigen and related antigens as a model system: A systematic approach for the determination of epitope specificities of monoclonal antibodies
19. Model‐building studies of antigen‐binding sites: The hapten‐binding site of MOPC‐315
20. A refined model for the variable domains (Fv) of the J539 β(1,6)‐D‐galactan‐binding immunoglobulin
21. A hypothetical space‐filling model of the V‐regions of the galactan‐binding myeloma immunoglobulin J539
22. A monoclonal antibody that defines an idiotype with two subsites in galactan‐binding myeloma proteins
23. The protein databank: A computer based archival file for macromolecular structure
24. Using known substructures in protein model building and crystallography
25. Canonical structures for the hypervariable regions of immunoglobulins
26. Conformations of immunoglobulin hypervariable regions
27. A 3D building blocks approach to analyzing and predicting structure of proteins
28. Prediction of the folding of short polypeptide segments by uniform conformational sampling
29. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
30. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
31. Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies ofMCPC603 from many randomly generated loop conformations
32. Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops
33. Conformational sampling using high temperature molecular dynamics
34. Modeling antibody hypervariable loops: A combined algorithm
35. Ring closure and local conformational deformation of chain molecules
36. Interactive computer graphics and representation of complex biological structures
37. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
38. Crystallographic refinement by simulated annealing: Application to crambin
39. Energy functions for peptides and proteins
40. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsion potentials for the naturally occurring amino acids
41. Solvation energy in protein folding and binding
42. Immunoglobulin transcripts and molecular history of a hybridoma that produces antibody to carcinoembryonic antigen
43. Tertiary templates for proteins
44. Equation of state calculations by fast computing machines
45. Knowledge based modeling of homologous protein, part II: Rules for the conformations of substituted side chains
46. An analysis of incorrectly folded protein models
47. Internal cavities and buried waters in globular proteins
48. On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands
49. Criteria that discriminate between native proteins and incorrectly folded models
50. The meaning of hydrophobicity
51. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
52. Evaluation of the dispersion contribution to the solvation energy. A simple computational model in a continuum approximation
53. On the calculation of electrostatic interactions in proteins
54. Protein folding and association: Insights from the interfacial and thennodynamic properties of hydrocarbons
55. Calculating the total electrostatic energies with the nonlinear Poisson‐Boltzman equation
56. Solvent‐accessible surfaces of proteins and nucleic acids