|
|
|
|
|
|
|
New Fuzzy Logic Strategies for Bio-molecular Recognition
|
|
The concepts of molecular similarity and molecular complementarity, playing
important roles in the broad field of molecular recognition, are chemical
problems, in which the eyeball technique used by a human observer is very
successful but which are very hard to code into a computer algorithm. Based
on the model of molecular surfaces, our new approach defines overlapping
surface patches with similar molecular properties. These patches are used to
represent local features of the molecule in a way, which is beyond the
atomistic resolution but can nevertheless be applied in partial similarity
as well as complementarity analyses in a very general sense. It can be shown
that this molecular description can be used as the first step in a docking
algorithm for complexes, where the structures of both molecules are known,
as well as for the identification of possible active sites without the
knowledge of specific molecules binding to this site.
|
|
|
References:
|
|
1)
|
Exner, T. E.; Brickmann, J. "New docking algorithm based on fuzzy set theory" J.Mol.Model. 3, 321-324 (1997).
|
|
2)
|
Exner, T. E.; Brickmann, J. "Fuzzy Logic Strategien zur Behandlung der Molekularen Erkennung" GIT Labor-Fachzeitschrift 11, 1144-1146 (1998).
|
|
3)
|
Exner, T. E.; Brickmann, J. "Molecular Shape Recognition Using Fuzzy Logic Strategies" Match - Communications in Mathematical and in Computer Chemistry 38, 53-80 (1998).
|
|
4)
|
Brickmann, J. and Exner, T. E. "Recognition Using Fuzzy Logic Strategies" in Chemistry Forum '99, Proceedings of the Vth International Symposium Warschau,15-23 (1999).
|
|
5)
|
Exner, T. E.; Brickmann, J. "The Identification of Complementarity of Molecular Surfaces Using Fuzzy Set Theory" J.Mol.Model. 7, 370-373 (2001).
|
|
6)
|
Exner, T. E.; Keil, M.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces I. Pattern Generation Using Fuzzy Set Theory" J.Comp.Chem. 23, 1176-1187 (2002).
|
|
7)
|
Exner, T. E.; Keil, M.; Brickmann, J. "Fuzzy Logic Strategies for the Treatment of the Molecular Recognition Problem" in Reviews in Modern Quantum Chemistry: A Celebration of the Contributions of Robert Parr; Sen, K. D. (Ed.); World Scientific Publ.: Singapore, 2002; pp 1735-1766.
|
|
8)
|
Exner, T. E.; Keil, M.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces II. Surface Complementarity" J.Comp.Chem. 23, 1188-1197 (2002).
|
|
9)
|
Exner, T. E.; Keil, M.; Brickmann, J. "Fuzzy Set Theory and Fuzzy Logic and Its Application to Molecular Recognition" in Chemoinformatics - From Data to Knowledge; Gasteiger, J., Engel, T. (Eds.); Wiley-VCH: Weinheim, 2003; pp 1216-1238.
|
|
10)
|
Keil, M., Exner, T. E., and Brickmann, J. "Prediction and classification of protein binding sites" in Abstracts of Papers; 226th ACS National Meeting, New York, NY, United States, September 7-11, 2003, (2003).
|
|
11)
|
Exner, T. E.; Keil, M.; Brickmann, J. "New Fuzzy Logic Strategies for Bio-molecular Recognition" SAR QSAR Environ.Res. 14, 421-431 (2003).
|
|
12)
|
Keil, M.; Exner, T. E.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces III. Binding Site Prediction with a Neural Network" J.Comp.Chem. 25, 779-789 (2003).
|
|
