Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and bench...

Docking and fusion of transport vesicles constitute elementary steps in intracellular membrane traffic. While docking is thought to be initiated by Rab-effector complexes, fusion is mediated by SNARE (N-ethylmaleimide-sensitive factor [NSF] attachment receptor) proteins. However, it has been recently debated whether SNAREs also play a role in the establishment or maintenance of a stably docked ...

Molecular docking programs play a crucial role in drug design and development. In recent years, much attention has been devoted to the protein-peptide docking problem in which docking of a flexible peptide with a known protein is sought. In this work we present a new docking algorithm which is based on the use of a filling function method for continuos constrained global optimization. Indeed, t...

In the last years, the importance of water molecules in pose prediction experiments has been widely recognized and several approaches to integrate water molecules into the docking process have been proposed [1,2]. The inclusion of water molecules extends the classical two-body problem of docking a flexible ligand into a protein receptor to a multi-body docking problem as protein-ligand, protein...

The goal of this work was to determine if it is feasible to use Mir/Shuttle docking data to perform Mir damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify physical characteristics of a structure which can subsequently be used for damage detection. The RSS method was demonstrated for a nume...

This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e....

Despite the importance of protein-RNA interactions in the cellular context, the number of available protein-RNA complex structures is still much lower than those of other biomolecules. As a consequence, few computational studies have been addressed towards protein-RNA complexes, and to our knowledge, no systematic benchmarking of protein-RNA docking has been reported. In this study we have extr...

This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e....

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function ar...

Receptor flexibility is a critical issue in structure-based virtual screening methods. Although a multiple-receptor conformation docking is an efficient way to account for receptor flexibility, it is still too slow for large molecular libraries. It was reported that a fast ligand-centric, shape-based virtual screening was more consistent for hit enrichment than a typical single-receptor conform...