Computational Drug Discovery and Design

The first line indicates that the pocket is composed of 68 patches and chemical features, shape, electrostatic potential, hydrog ...

Running the scripts will generate a directory, for each ligand in the ligand list in thelig_prep.infile, each of which contains ...

python compare_seeds.py [Input file] PLPS_path ~/project/PL-PatchSurfer2/ receptor_file rec.ssic n_conf 50 ligand_dir ZINC038338 ...

Another output is a summary file provided for each ligand screened. It is named as a combination of the receptor file name and t ...

An example of an input file is illustrated below (lcs.inprovided in theexampledirectory): receptor_file rec.ssic scoring_type lc ...

patches and ranking ligands. Four parameters should be given to run the python script. python gen_input.py [Receptor SSIC] [PL-P ...

Table1 shows top 18 (1%) ranked ligands. Two-dimensional struc- tures of the molecules are shown in Fig.6. Among top 18 mole- cu ...

cognate ligand of the template structure as the input parameter used in Subheading3.1. If there are no homologous structures tha ...

Acknowledgment We acknowledge Dan K. Ntala for proofreading the manuscript. This work was partly supported by grants from the Na ...

protein databank and Cambridge Structural Database. J Chem Info Model 50(4):572–584 Sael L, Kihara D (2012) Detecting local lig ...

Chapter 8 Fragment-Based Ligand Designing Shashank P. Katiyar, Vidhi Malik, Anjani Kumari, Kamya Singh, and Durai Sundar Abstrac ...

building material to start with and develop novel blocks with drug- like properties. Next, developed blocks are screened for the ...

engineering techniques need to keep all the good properties of the molecules to further identify and remove the unwanted propert ...

sampling of the search space optimally. The performance of any software depends on how well it performs these three basic opera- ...

In the absence of target structure, LBDND approach can be used by gathering constraints from the known active and inactive ligan ...

The existing receptor–ligand information is explored and exploited to generate frequency database of each possible atom pairs an ...

depth-first search’, ‘Monte Carlo and Metropolis criterion’ and ‘Evolutionary algorithms’ [36, 39, 43, 44]. After the briefings ...

atom types helps in determining the parameters to be used for each atom. If the protein is considered to be static and frag- men ...

perform single point calculation as the geometry of the frag- ment is already known [52].The combination of 6-31G(d) set [53] an ...

includes all the information required to runPOCKET. Simple command line for runningPOCKETis: #Pocket parameter_file.index Parame ...