Finding biologically relevant protein domain interactions: Conserved binding mode analysis

Cloning of conserved regions of nontypeable Haemophilus influenzae hmw1 core binding domain

Colonization of nontypeable Haemophilus influenzae (NTHi) in nasopharynx causes respiratory tract disease. In 80% of clinical isolates, HMW proteins are the major adhesions and induce protective antibodies in the hosts. Therefore, it can be used as a vaccine candidate. The aim of this study is designing and cloning of the conserved regions of NTHi hmw1 core binding domain.In this study, the sta...

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites

The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by computational approaches using available data on protein structural complexes. Recently we developed an approach called IBIS (Inferred Biomolecular In...

Arbitrary protein−protein docking targets biologically relevant interfaces

BACKGROUND Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this re...

Cooperativity in noncovalent interactions of biologically relevant molecules.

Using a recently published benchmark MP2 database of nucleic acid base trimers, the three-body contribution to the interaction energy (TBE, also termed (non)cooperativity) as a function of base composition and complex geometry is studied. In 28 out of 141 cases (or 20%), the counterpoise-corrected MP2/TZV(2df,2pd) TBE exceeds 1 kcal mol(-1). The TBE is below 1 kcal mol(-1) for all trimers in th...

Evaluating and Utilizing Weak Interactions in Biologically Relevant Systems