Release 0.7.1

This release contains new features:

• It is possible now to specify only restraints in the ligand partner.
• Protein-DNA docking protocol has been tested and fixed, including a memory leak in the scoring function and the clustering BSAS post-script.
• Support in fastdfire for membrane beads (MMB) for explicit membrane docking.

Release 0.7.0

Changes on this release have been tracked in the following issues:

• Check atoms in PDB parser (#18), which also adds the new flags to setup --noh, --verbose_parser and fixes the behavior of --noxt flag.
• Fix for bug in ANM calculation which was not using parsed structures (#19).
• Implementation for all the available scoring functions of the restraints mechanism (#20).
• Tests for all the post scripts (#21).
• DNA scoring function has been also updated and now supports residue restraints (#22). DNA scoring function is still under development.

Release 0.6.0

Residue restraints support, ANM model can be disabled for specific partners, post-filtering with diverse restraint source.

Release 0.5.6

• More comprehensive documentation has been added, specially for residue restraints support (see 4G6M example).
• A script for executing parallel tasks has been added (Ant-Thony).

Release 0.5.5

This release adds support for active and passive residue restraints. Both active and passive residues are used for filtering out swarms (receptor) and pre-orienting ligand poses to face restraints on receptor surface. Active residues are only used during the scoring of a given pose, which adds the percentage of satisfied restraints to the energy.

Release 0.5.4

Change log:

• Fixed quaternion random orientations to be biased when restraints on both receptor and ligand applies.
• Minor fixes

Release 0.5.3

• Multiple performance updates contributed by @Kintukp
• More tests on restraints support

Release 0.5.2

Full restraints support in both receptor and ligand has been implemented

• Restraints are specified as residues using the original numeration from the PDB input structures.
• Total number of swarms is filtered on the distance to residues in the receptor surface.
• During the simulation, the energy is biased depending on the percentage of restraints satisfied.
• The script lgd_filter_restraints.py is intended for filtering out structures predicted which don't satisfy the input restraints.

Release 0.5.1

Receptor distance restraints implemented as a pre-filter of closest swarms to interesting residues.

Release 0.5.0

This is a release which with no backward compatibility with previous versions.

It includes a new setup step, lightdock_setup command, previous to running the simulation.

Please, refer to the new documentation for more details.