BioMolTech: What's New in BioMolTech Lead Finder v.1.1.12

New	Lead Finder can now prepare protein models for docking. The model preparation includes the addition of hydrogen atoms to protein according to the ionization states of residues at a given pH, the extraction of a reference ligand for energy grid calculations, and assembling crystallographic units located within a given distance from the reference ligand.
New	New protein model preparation mode, initiated by the -build parameter: add missing hydrogen atoms, assign ionization states and bond types, remove docked ligand (if present), save the prepared protein structure model into a file and exit.
New	New execution parameter, -addH=[auto\|on\|off]. Setting this parameter to "on" forces the addition of missing hydrogen atoms and assignment of ionization states to the given protein structure at a certain pH value. When set to "off", the protein structure is taken "as is". When this parameter is not specified or set to "auto", Lead Finder tries to guess if the protein model needs to be prepared and if necessary, forces the addition of missing hydrogen atoms and assignment of ionization states to the protein structure.
New	New execution parameter: -xref [ resname NAME \| resnum X [Y] \| chain Z ]. This parameter provides an alternative method of specifying position and dimensions of the active center when a reference ligand or coordinates of the active center are not immediately available. This parameter can be used to automatically detect ligand in the protein structure, extract a named ligand from the protein structure, extract residue X as a ligand, extract residues X to Y as a ligand, or extract chain Z as a ligand, provided that it has no more than 500 non-hydrogen atoms.
New	New execution parameter: -cryst X. Assemble crystallographic subunits located within X Å from the reference ligand.
New	New execution parameter: -pH X. Specify pH value at which the protein model must be ionized.
New	New execution parameter: --poolsize=X. Increase the number of individuals in the initial pool by the factor of X. Lead Finder automatically determines the appropriate number of individuals in the initial pool based on the number of the conformational degrees of freedom, the energy grid size and other factors; setting X to a value other than one will alter the automatically determined number of individuals in the initial pool.
New	New execution parameter: --popsize=X. Increase the number of individuals in a population by the factor of X. Lead Finder automatically determines the appropriate number of individuals in a population based on a number of factors; setting X to a value other than one will alter the automatically determined number of individuals in the population.
New	New execution mode: --score-only. In this mode, dG and VS scores are calculated for a fixed ligand position and its locally optimized position. The scores and 3D positions of both initial and locally optimized positions are saved into X_report.log и X_docked.pdb.
New	The molar mass, the number of freely rotatable bonds between heavy atoms and the number of ligand's heavy atoms have been added in separate fields to the output of check-only mode and regular docking reports.
New	The Ligand Efficiency (LE) ratio has been added to the standard docking report output.
New	The check-only output can now be directed into a file specified in either the command line or the par file.
Improved	Conformation sampling of ligand with conjugated sp2-systems has been improved to increase docking accuracy.
Improved	Geometry of flat NH2 groups, connected to sp2-hybridized carbon, is corrected prior to docking: these groups are rotated so that the hydrogen atoms lie in one plane with other atoms connected to the sp2-hybridized carbon.
Improved	Bond between sp2-hybridized carbon and sp2-hybridized NH2 group is made non-rotatable.
Fixed	Rotation of the bond between carbonyl carbon and NHO group can be regulated by the "--rotate-conjugated" command line parameter.
Improved	Temporary data for parallel processes are stored in user’s temporary directory.
Improved	Example files are installed into user’s home directory instead of the "Program Files" hierarchy.
Improved	The dG and VS score algorithms have been improved to increase accuracy of prediction of the energy of hydrogen bonds formed by sulphur atoms
Improved	Numerous enhancements to the dG and VS scoring functions aimed at increasing accuracy of predictions
Fixed	Coordinates of a ligand that is covalently attached to the protein are generated incorrectly with user-specified length of the covalent bond.
Fixed	Setting bond length for covalent ligand docking does not work properly when ligand is docked to a pre-computed energy grid.
Improved	Enhancements to the calculations of free energy of coordination interaction of Na and Ni atoms with acceptor atoms, such as O, N and S.
Fixed	--grid-npoints parameter is now interpreted correctly.