Krahasoni metodat

	Lidhja Molekulare	Modelimi i Homologjisë	Modelimi i Farmakoforës	Topologjia e rrjetit PPI
Fusha	Bioinformatikë	Bioinformatikë	Bioinformatikë	Bioinformatikë
Familja	Process / pipeline	Process / pipeline	Process / pipeline	Process / pipeline
Viti i origjinës	1982	1993	1977	2000
Krijuesi	Irwin Kuntz	Andrej Sali	Peter Gund	Peter Uetz
Lloji	Binding prediction pipeline	Comparative structure prediction pipeline	Pattern-based virtual screening pipeline	Network analysis pipeline
Burimi themelues	Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982). A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology, 161(2), 269-288.	Sali, A. & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779-815.	Wermuth, C. G., Ganellin, C. R., Lindberg, P., & Mitscher, L. A. (1998). Glossary of terms used in medicinal chemistry. Pure and Applied Chemistry, 70(5), 1129-1143.	Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., ... & Lomax, J. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403(6770), 623-627.
Emërtime të tjera	protein-ligand docking, binding prediction	comparative modeling, template-based modeling	pharmacophore pattern recognition, 3D pharmacophore	protein interaction networks, interactome analysis, network topology
Të lidhura	4	4	3	3
Përmbledhja	Molecular docking predicts the preferred binding orientation and affinity of a ligand (small molecule) within a protein binding pocket. Pioneered by Kuntz and colleagues in 1982, this computational method searches conformational space to find energetically favorable ligand-protein complexes, enabling rapid screening of chemical libraries for drug discovery.	Homology modeling, also called comparative modeling, predicts the three-dimensional structure of a protein using an experimentally-solved structure of a homologous protein as a template. Introduced by Sali and Blundell in 1993, this method exploits the principle that homologous proteins share similar spatial structures despite differing in amino acid sequence.	Pharmacophore modeling identifies the spatial arrangement of molecular features (hydrogen bond donors, acceptors, aromatic rings) that are essential for biological activity. Introduced by Gund in 1977, this ligand-based method creates a three-dimensional pattern that can screen chemical libraries and design new active compounds without requiring receptor structure.	Protein-protein interaction network analysis identifies and characterizes the structural properties of cellular interaction networks. Pioneered by Uetz and colleagues through large-scale yeast two-hybrid screening, this approach reveals topological features like hubs, modules, and motifs that encode functional organization and disease associations.