HOMCOS 1.0 : HOmology Modeling of protein COmplex Structure

A Serever to Predict Binding Sites and Protein Pairs of Protein-Protein Interaction
by Homology Modeling of Complex Structures

	Modeling heterodimer	:Modeling a heterodimeric 3D structure from two query sequences
	Modeling homodimer	:Modeling a homodimeric 3D structure from one query sequence
	Idenfifying putative interacting proteins	:Identifying putative interacting proteins in Uniprot database for one query sequence.

• Fukuhara N., Kawabata T. "HOMCOS: A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures". Nucleic Acids Research, Web server issue (2008), 36(Web Server issue):W185-W189. [PubMed] [NAR]

• Fukuhara N., Go N. and Kawabata T.
  "Prediction of Interacting Proteins from Homology-modeled Complex Structure Using Sequence and Structure Scores" BIOPHYSICS, Vol.3 (2007), pp 13.

Homology to a known 3D structure of a protein complex is a powerful tool to predict new interaction and interaction sites. However, please note following two points:

• Interaction specificities among many homologous protein pairs are generally difficult to predict.

• A pair of protein dimer 3D structures with less than 30-40 sequence identity sometimes show a diffrent structural topology. If a generated 3D model is based on a remote homologous template strucutre, please be careful to use it.

Lab for Structural and Functional Bioinformatics