MIAX: A new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases

Proteins: Structure, Function and Genetics

Volumn 48, Issue 4, 2002, Pages 696-732

  Del Carpio Muñoz, Carlos Adriel ^a   Ichiishi, Eiichiro ^b   Yoshimori, Atsushi ^a   Yoshikawa, Toshikazu ^b  

^a TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

^b KYOTO PREFECTURAL UNIVERSITY OF MEDICINE   (Japan)

Author keywords

Docking; Epitopes; Filtering; Modeling; Protein complex; Protein interaction; Self organizing map or Kohonenen networks; Simulated annealing

Indexed keywords

ALGORITHM; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPLEX FORMATION; ELECTRICITY; ENERGY; HYDROPHOBICITY; LIQUID CRYSTAL; MACROMOLECULE; MOLECULAR MODEL; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; VALIDATION PROCESS;

ALGORITHMS; AMINO ACIDS; ANIMALS; BINDING SITES; CHYMOTRYPSINOGEN; COMPUTATIONAL BIOLOGY; ELECTROSTATICS; HUMANS; HYDROPHOBICITY; LEUKOCYTE ELASTASE; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OVOMUCIN; PROTEIN BINDING; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SOLVENTS; TRYPSIN INHIBITOR, KAZAL PANCREATIC; UBIQUITINS;

EID: 0036721521     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10122     Document Type: Article

References (46)

1. Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-immunity protein complexes
2. Quantifying biological specificity: The statistical mechanics of molecular recognition
3. Elusive affinities
4. The kinetics of protein-protein recognition
5. Protein-protein interaction at crystal contacts
6. Protein docking and complementarity
7. Protein-protein recognition analysed by docking simulation
8. Docking by least-squares fitting of molecular surface patterns
9. New algorithm to model protein-protein recognition based on surface complementarity
10. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
11. A geometry-based suite of molecular docking processes
12. Atomic solvation parameters in the analysis of protein-protein docking results
13. Solvation energy in protein folding and binding
14. Hydrophobicity of amino acid subgroups in proteins
15. Prediction of protein complexes using empirical free energy functions
16. Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
17. Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction
18. Prediction of protein complexes using empirical free energy functions
19. Modelling protein docking using shape complementarity, electrostatics and biochemical information
20. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy
21. "Soft docking": Matching of molecular surface cubes
22. Bigger: A new (soft) docking algorithm for predicting protein interactions
23. Protein docking using spherical polar Fourier correlations
24. A role for surface hydrophobicity in protein-protein recognition
25. Distribution and complementarity of hydropathy in multisubunit proteins
26. Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
27. The self-organizing map
28. Differentiation of lipid-associating helices by use of three dimensional molecular hydrophobicity potential calculations
29. Electrostatic contributions to protein-protein binding affinities: Application to rap/raf interaction
30. Simulating proton translocations in proteins: Probing proton transfer pathways in the rhodobacter sphaeroides reaction center
31. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
32. Solvent-accessible surfaces of proteins and nucleic acids
33. Aspects of statistical thermodynamics of real fluids
34. An improved algorithm for the analytical computation of solvent-excluded volume. The treatment of singularities in solvent-accessible surface area and volume functions
35. The multivariate calibration problem in chemistry solved by the PLS method
36. Semianalytical treatment of solvation for molecular mechanics and dynamics
37. General parameterized SCF model for free energies of solvation in aqueous solution
38. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
39. Affinity and specificity of serine endopeptidase-protein inhibitor interactions
40. The interpretation of protein structures: Estimation of static accessibility
41. Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for hydrophobic effect
42. MSEED: A program for rapid analytical determination of accessible surface areas and their derivatives
43. A parallel genetic algorithm for polypeptide three dimensional structure prediction. A transputer implementation
44. The atomic structure of protein-protein recognition sites