Current State-of-the-art for Virtual Screening and Docking Methods - New Developments in Medicinal Chemistry - page 102

VinaMPI facilitates multiple receptor high-throughput virtual docking on high-
performance computers (leadership-class computing resources), using a large
number of cores to decrease the time-to-completion of the screen. It is a massively
parallel Message Passing Interface (MPI) program based on multithreaded virtual
docking programs and used to distribute tasks. Multithreading can be used to
speed-up individual docking tasks. It uses a distribution scheme in which tasks are
evenly distributed to the workers based on the complexity of each task defined by
the number of rotatable bonds in each chemical compound. In can handle
efficiently multiple proteins in a ligand screen. High-throughput inverse docking
is allowed [532].
PBVS+DBVS a structure-based pharmacophore (SBP)-guided method was
suggested to generate comprehensive pharmacophores of a number of crystal
structures of target-inhibitor complexes. It is a hybrid protocol of a virtual
screening method, comprised of pharmacophore model-based virtual screening
(PBVS), rigid and flexible docking-based virtual screenings (DBVS). The
Protocol is used for retrieving new inhibitors from commercially available
chemical databases [533],
Grid-based FPS is a grid-based molecular footprint comparison method for
docking and de novo design . It is a multigrid implementation of the footprint
similarity (FPS), scoring function (useful for identification of compounds that
binds to a protein on a per-residue basis). The method is faster than its Cartesian-
space counterpart that is good for on-the-fly docking, de novo design or virtual
screening.It is used to tailor construction of new molecules to have specific
properties [534].
Forecaster is platform for drug discovery that fully integrates computations,
virtual, theoretical and medicinal (experimental, intuitive) chemistry to take
advantage of the full potential of these approaches. It is a web-based platform and
a number of programs (Prepare, React, Select) with the objective of combining
medicinal chemistry and computational chemistry expertise in order to facilitate
drug discovery and development. It specifically aims to integrate synthesis into
computer-aided drug design. The platform is used to build virtual combinatorial
libraries, filter and extract a highly diverse library from databases and dock them