Arumay Pal

TL;DR: The weak dimer interfaces may be good models in terms of their size, composition, and evolutionary conservation for the labile subunit contacts that allow protein assemblies to share and exchange components, allosteric proteins to undergo quaternary structure transitions, and molecular machines to operate in the cell.

TL;DR: ProFace is a suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits and can be used to infer if a particular interface belongs to a homodimeric molecule.

TL;DR: A newly developed energy-based coarse-grained model was successfully applied to predict the structure of ssDNA–ssDBP and ssRNA–ssRBP complexes and to assess their sequence-specific interactions and stabilities and tuned two factors that can modulate specific recognition: base–aromatic stacking strength and the flexibility of the single-stranded nucleic acid.

TL;DR: Dominant segments involved in specific interactions, along with their secondary structural features, are enumerated and can be used as one of the parameters to distinguish between the two types of interfaces.

TL;DR: A set of four parameters that in combination can predict DNA-binding residues on protein structures to a high degree of accuracy are presented: number of evolutionary conserved residues and their spatial clustering, hydrogen bond donor capability and residue propensity, and SVM approach for recognizing the interface region.