Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and...

Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the...

Few methods use molecular dynamics simulations based on atomically detailed force fields to study the proteinligand docking process because they are considered too time demanding despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics simulations which has a highly flexible computational granularity. We compare the accuracy and the time required with wel...

The idea in molecular docking is to design pharmaceuticals computationally by identifying potential drug candidates targeted against proteins. The candidates can be found using a docking algorithm that tries to identify the bound conformation of a small molecule ligand to a macromolecular target at its active site, which is the region of an enzyme where natural substrate binds. Mathematically, ...

Few methods use molecular dynamics simulations in concert with atomically detailed force fields to perform protein–ligand docking calculations because they are considered too time demanding, despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics which has a highly flexible computational granularity. We compare the accuracy and the time required with wel...

Different groups in our community hold strong views about tail docking in domestic dogs. These range from veterinary associations and welfare organisations, which typically want the practice banned, to purebred dog associations, which vigorously oppose the introduction of antidocking legislation. An evaluation of the tail docking issue, which is informed and nonemotive, requires the integration...

Evaluation of Surface Complementarity, Hydrogen bonding, and Electrostatic interaction in molecular Recognition (ESCHER) is a new docking procedure consisting of three modules that work in series. The first module evaluates the geometric complementarity and produces a set of rough solutions for the docking problem. The second module identifies molecular collisions within those solutions, and th...

Protein–ligand docking is the major workhorse in computeraided structure-based lead finding and optimization. Predicted protein–ligand complex configurations are used for studying protein–ligand interactions, estimating binding affinities, and as a final filter step in virtual screening. Early methods on protein–ligand docking treated either both proteins and ligands as rigid molecules or allow...

We here approach the problem of designing a controller for automatic rendezvous and docking (AR&D). As a first step towards a fully reactive neurocontroller (based on state feedback), an artificial neural network is trained offline by a fitness based genetic algorithm to fulfill the docking task. Its performance using one specific docking case, with fixed initial and boundary conditions, is com...