Protein–ligand interactions are the fundamental basis for molecular design in
pharmaceutical research, biocatalysis, and agrochemical development. Especially hydrogen …

Motivation: The increasing amount of data on protein–protein interaction needs to be
rationalized for deriving guidelines for the alteration or design of an interface between two …

Specific protein-protein interactions are essential for cellular functions. Experimentally
determined three-dimensional structures of protein-protein complexes offer the possibility to …

Empirical residue–residue pair potentials are used to screen possible complexes for protein–
protein dockings. A correct docking is defined as a complex with not more than 2.5 Å …

Rapid accumulation of experimental data on protein‐protein complexes drives the paradigm
shift in protein docking from “traditional,” template free approaches to template based …

MOTIVATION: New software has been designed to assist the molecular biologist in
understanding the structural consequences of modifying a ligand and/or protein. RESULTS …

Highlights•The most accurate complex models are built by copying close homologous
templates.•Non-homologous templates can be detected by interface structure comparisons.• …

Protein surface regions with similar physicochemical properties and shapes may perform
similar functions and bind similar binding partners. Here we present two web servers and …

Protein–protein interactions are ubiquitous, essential to almost all known biological
processes, and offer attractive opportunities for therapeutic intervention. Developing small …

Analysis of proteins commonly requires the partition of their structure into regions such as
the surface, interior, or interface. Despite the frequent use of such categorization, no …