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« LigandScout 3.1 Overview 1. Help Overview 2. Introduction to LigandScout 2.1 What's New in LigandScout 3? 2.2 Installing and Starting LigandScout 2.3 Visual Semantics 2.4 LigandScout Graphical User Interface 3. File Handling, Data Management and Networking 3.1 Importing and Exporting Files 3.2 Retrieving PDB Complexes Online 3.3 Local and Shared Repository 3.4 Sessions 3.5 Networking 4. LigandScout Perspectives 4.1 Basic User Interface Modules 4.2 Structure-Based Modeling Perspective 4.3 Ligand-Based Modeling Perspective 4.4 Alignment Perspective 4.5 Screening Perspective 5. Introduction to Pharmacophore Modeling 5.1 Pharmacophore Modeling 5.2 Pharmacophore Feature Definitions 5.3 Editing a Pharmacophore Model 6. Structure-Based Pharmacophore Design 6.1 Structure-Based Pharmacophores 6.2 Creating Structure-Based Pharmacophores 7. Pharmacophore Alignment 7.1 Aligning Pharmacophores and Molecules 7.2 Shared Feature Pharmacophore 7.3 Merged Feature Pharmacophore 8. Ligand-Based Pharmacophore Design 8.1 Ligand-Based Pharmacophores 8.2 Creating Ligand-Based Pharmacophores 9. Virtual Screening 9.1 Virtual Screening in LigandScout 9.2 Preparing a Pharmacophore for Virtual Screening with External Applications 10. LigandScout Settings: Preferences 10.1 Structure-Based Modeling Settings 10.2 Ligand-Based Modeling Settings 10.3 Chemistry Settings 10.4 Library Screening Settings 10.5 Alignment Settings 10.6 Rendering Settings 10.7 Program and Network Settings A. Appendix A.1 LigandScout Menu Reference A.2 LigandScout Icons Reference A.3 LigandScout Keyboard Shortcuts A.4 LigandScout Mouse Bindings A.5 Network Administrator Guide A.6 Command Line Usage A.7 Scoring Function A.8 Calculation of MMFF94 Binding Enthalpies A.9 Primary Literature Index	Table of Contents 1. Help Overview 2. Introduction to LigandScout What's New in LigandScout 3? Installing and Starting LigandScout Visual Semantics LigandScout Graphical User Interface 3. File Handling, Data Management and Networking Importing and Exporting Files Retrieving PDB Complexes Online Local and Shared Repository Sessions Networking 4. LigandScout Perspectives Basic User Interface Modules Structure-Based Modeling Perspective Ligand-Based Modeling Perspective Alignment Perspective Screening Perspective 5. Introduction to Pharmacophore Modeling Pharmacophore Modeling Pharmacophore Feature Definitions Editing a Pharmacophore Model 6. Structure-Based Pharmacophore Design Structure-Based Pharmacophores Creating Structure-Based Pharmacophores 7. Pharmacophore Alignment Aligning Pharmacophores and Molecules Shared Feature Pharmacophore Merged Feature Pharmacophore 8. Ligand-Based Pharmacophore Design Ligand-Based Pharmacophores Creating Ligand-Based Pharmacophores 9. Virtual Screening Virtual Screening in LigandScout Preparing a Pharmacophore for Virtual Screening with External Applications 10. LigandScout Settings: Preferences Structure-Based Modeling Settings Ligand-Based Modeling Settings Chemistry Settings Library Screening Settings Alignment Settings Rendering Settings Program and Network Settings A. Appendix LigandScout Menu Reference LigandScout Icons Reference LigandScout Keyboard Shortcuts LigandScout Mouse Bindings Network Administrator Guide Command Line Usage Scoring Function Calculation of MMFF94 Binding Enthalpies Primary Literature Index
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Page designed & authored by G. Wolber

Inte:Ligand: Your partner for in-silico drug discovery

Start Science & Technology Products & Services Company Career Contact

« LigandScout 3.1 Overview

1. Help Overview

2. Introduction to LigandScout

2.1 What's New in LigandScout 3?
2.2 Installing and Starting LigandScout
2.3 Visual Semantics
2.4 LigandScout Graphical User Interface

3. File Handling, Data Management and Networking

3.1 Importing and Exporting Files
3.2 Retrieving PDB Complexes Online
3.3 Local and Shared Repository
3.4 Sessions
3.5 Networking

4. LigandScout Perspectives

4.1 Basic User Interface Modules
4.2 Structure-Based Modeling Perspective
4.3 Ligand-Based Modeling Perspective
4.4 Alignment Perspective
4.5 Screening Perspective

5. Introduction to Pharmacophore Modeling

5.1 Pharmacophore Modeling
5.2 Pharmacophore Feature Definitions
5.3 Editing a Pharmacophore Model

6. Structure-Based Pharmacophore Design

6.1 Structure-Based Pharmacophores
6.2 Creating Structure-Based Pharmacophores

7. Pharmacophore Alignment

7.1 Aligning Pharmacophores and Molecules
7.2 Shared Feature Pharmacophore
7.3 Merged Feature Pharmacophore

8. Ligand-Based Pharmacophore Design

8.1 Ligand-Based Pharmacophores
8.2 Creating Ligand-Based Pharmacophores

9. Virtual Screening

9.1 Virtual Screening in LigandScout
9.2 Preparing a Pharmacophore for Virtual Screening with External Applications

10. LigandScout Settings: Preferences

10.1 Structure-Based Modeling Settings
10.2 Ligand-Based Modeling Settings
10.3 Chemistry Settings
10.4 Library Screening Settings
10.5 Alignment Settings
10.6 Rendering Settings
10.7 Program and Network Settings

A. Appendix

A.1 LigandScout Menu Reference
A.2 LigandScout Icons Reference
A.3 LigandScout Keyboard Shortcuts
A.4 LigandScout Mouse Bindings
A.5 Network Administrator Guide
A.6 Command Line Usage
A.7 Scoring Function
A.8 Calculation of MMFF94 Binding Enthalpies
A.9 Primary Literature

Index

Command Line Usage

The generation of conformations, ligand-based pharmacophores and the screening of molecule libraries can be called from the command line. The executables are located in the LigandScout installation directory.

Conformation Generation

Usage:

idbgen [Mandatory arguments] [Optional arguments] [Distribution arguments]

Mandatory arguments:

--input, -i {infile}		input file (.sdf, .smi, .mol2, .ldb)
--output, -o {outfile}		output file (*.ldb)

Optional arguments:

--help, -h {helptype}		command line parameter help
helptype:	all	lists all arguments
	simple	shows most important arguments
	distribution	shows network arguments
	[param]	displays detailed help for the argument '[param]'
--sysinfo		system information
--log-file, -l {logfile}		output file for logging-messages (default: stdout)
--confgen-type, -t {type}		confgen type (default: omega-fast)
type:	omega-fast	omega high-throughput settings (25 confs)
	omega-best	omega high-quality settings (500 confs)
	import	import from input file
--multi-conf, -m {type}		auto-sense conformations in SDF files (default: off)
type:	name	auto-sense by name comparison
	structure	auto-sense by structure-hash comparison
--num-confs, -n {number}		max. number of conformations to generate (default set by '--confgen-type' option)
--name-property, -p {propname}		property for overriding molecule name
--omega-license, -z {file}		omega license file (default: file specified by environment variable OE_LICENSE)
--hydrophob-threshold, -T {number}		the minimal surface accessibility threshold for hydrophobicity (default: 0.25)
--error-file, -e {file}		file that collects molecules where errors occurred (default: {OUTPUT_FILE}-failed.log)
--update-keep-old, -K		update database and keep old entries
--update-drop-old, -R		update database and drop old entries
--allow-duplicates, -A		allow duplicates in the database (default: off)
--overwrite-existing, -O		overwrite already existing molecules (default: off)
--num-processes, -b {#processes}		number of processes to start (default: number of CPUs)
--first-index, -F {index}		first molecule index to use (default: 1)
--last-index, -L {index}		last molecule index to use (default: library-size)
--index-file, -I {file}		file containing input molecule-indexes to use (default: all molecules)
--end-time, -E {time}		task is stopped when end-time is reached (default: no time limit)
--process-time, -P {time}		max amount of time this process is executed (default: no time limit)
--input-db, -D {file}		input database (*.ldb) to use additionally to the input library.
--start-positions, -S {file}		compound start positions file of the input library.
--exec-mode, -x {mode}		the execution mode (default: multi)
mode:	single	only one CPU is used
	multi	uses all CPUs/cores of this computer
	network	uses computers in the network

Distribution options:

--host-list-file, -H {file}		host list file (default: ${HOME}/.inteligand-data/ligandscout3/iworker-list.txt)
--comma-sep-hosts, -c {list}		comma separated host list (HOST1:PORT1,HOST2:PORT2,...)
--network-interface, -N {name}		network interface to use ('-N list' to list all available interfaces)
--verbosity, -v {loglevel}		network logging verbosity (default: off)
loglevel:	off	no network log messages
	low	network errors and warnings
	medium	connection info messages are shown
	high	high-level protocol messages
	highest	debug (very verbose)
--kill-workers, -X		kill iworkers when finished (default: off)

Ligand-based Pharmacophore Generation

Usage:

espresso [Mandatory arguments] [Optional arguments]

Mandatory arguments:

--training-set, -t {filen}

input file containing the training-set (*.sdf, *.mol2, *.ldb, *.smi)

Optional arguments:

--input, -i {file}		input file containing the training- and/or test-set (*.lsd)
--help, -h {helptype}		command line parameter help
helptype:	all	lists all arguments
	simple	shows most important arguments
	[param]	displays detailed help for the argument '[param]'
--sysinfo		system information
--quiet, -q		suppress logging and info messages
--log-file, -l {logfile}		output file for logging-messages (default: stdout)
--test-set, -s {file}		input file containing the test-set (.sdf, .mol2, .ldb, .smi)
--pharmacophore, -p {file}		output file containing the generated pharmacophore (.pmz, .pml)
--output, -o {file}		output file for training-set ligands that were used for pharmacophore generation (.sdf, .mol2, .ldb, .smi, *.lsd)
--confgen-type, -c {type}		confgen type (default: omega-fast)
--num-confs, -n {number}		max. number of conformations to generate (default set by '--confgen-type' option)
--omega-license, -z {file}		omega license file (default: file specified by environment variable OE_LICENSE)
--keep-confs, -y		keep input conformations (default: override)
--disable-excluded-volumes, -x		generate exclusion volumes from training-set
--pharmacophore-type, -g {type}		the type of the pharmacophore to generate (default: merged)
type:	shared	shared feature pharmacophore
	merged	merged feature pharmacophore
--scoring-function, -f {score}		the function to use for scoring intermediate solutions and resulting pharmacophores (default: combo)
score:	pharma_fit	scores the number of matching pharmacophore features and the RMSD of the pharmacophore alignment
	fast_shape	scores the atom van der Waals sphere overlap of the aligned training-set molecules
	shape	scores the molecular shape similarity of the aligned training-set molecules based on a gauss function representation of the molecular volume
	combo	scores the number of matching pharmacophore features, the RMSD of the pharmacophore alignment and the atom van der Waals sphere overlap of the aligned training-set molecules
--intermediate, -r {number}		the number of intermediate alignment solutions to use (default: 10)
--tolerance, -e {number}		the global feature tolerance scaling factor (default: 1.0)
--merged-omit, -m {number}		max. omitted features for merged feature pharmacophores (default: 4)
--mark-optional-features, -k		mark partially matching features as optional (default: enabled)
--optional-feature-t, -d {number}		optional feature threshold (default: 10%)
--pharm-name-prefix, -u {prefix}		name-prefix for resulting pharmacophore(s) (default: Model)

Virtual Screening

Usage:

iscreen [Mandatory arguments] [Optional arguments] [Distribution arguments]

Mandatory arguments:

--query, -q {file}		query pharmacophore (.pmz,.pml)
--database, -d {file}		database to screen (*.ldb)
--output, -o {file}		hit list (.sdf, .ldb)

Optional arguments:

--help, -h {helptype}		command line parameter help
helptype:	all	lists all arguments
	simple	shows most important arguments
	distribution	shows network arguments
	[param]	displays detailed help for the argument '[param]'
--sysinfo		system information
--log-file, -l {logfile}		output file for logging-messages (default: stdout)
--disable-first-match-mode, -s		all matching conformations are considered (default: only first matching)
--regex-file, -r		file with regular expressions to select molecules from database.
--disable-exclusion-volumes, -e		disable checking for exclusion volume clashes
--fragment-screening-mode, -f		enable fragment screening mode
--allow-omit, -a		maximum number of features to omit (default: 0)
--min-required, -m		minimum number of required features (default: 3)
--first-index, -F {index}		first molecule index to use (default: 1)
--last-index, -L {index}		last molecule index to use (default: library-size)
--end-time, -E {time}		task is stopped when end-time is reached (default: no time limit)
--process-time, -P {time}		max amount of time this process is executed (default: no time limit)
--num-cores, -C {number}		max amount of cores used by this process (default: all cores)
--timeout-cl, -T {time}		execution time-out on compound level (default: disabled)
--exec-mode, -x {mode}		the execution mode (default: multi)
mode:	single	only one CPU is used
	multi	uses all CPUs/cores of this computer
	network	uses computers in the network

Distribution options:

--host-list-file, -H {file}		host list file (default: ${HOME}/.inteligand-data/ligandscout3/iworker-list.txt)
--comma-sep-hosts, -c {list}		comma separated host list (HOST1:PORT1,HOST2:PORT2,...)
--network-interface, -N {name}		network interface to use ('-N list' to list all available interfaces)
--verbosity, -v {loglevel}		network logging verbosity (default: off)
loglevel:	off	no network log messages
	low	network errors and warnings
	medium	connection info messages are shown
	high	high-level protocol messages
	highest	debug (very verbose)
--kill-workers, -X		kill iworkers when finished (default: off)

Networking: iworker

Usage:

iworker [Optional arguments]

Optional arguments:

--help, -h {helptype}		command line parameter help
helptype:	all	lists all arguments
	simple	shows most important arguments
	[param]	displays detailed help for the argument '[param]'
--sysinfo		system information
--log-file, -l {logfile}		output file for logging-messages (default: stdout)
--auto-detection, -a		enable auto-detection (default: off)
--max-parallel-tasks, -m {number}		maximum number of parallel executed tasks (default: number of CPUs)
--max-load, -d {number}		maximum cpu load (1-100) (default: disabled)
--network-interface, -N {name}		network interface to use ('-N list' to list all available interfaces)
--port, -p {number}		tcp server port to use (default:30000)
--verbosity, -v {loglevel}		network logging verbosity (default: off)
loglevel:	off	no network log messages
	low	network errors and warnings
	medium	connection info messages are shown
	high	high-level protocol messages
	highest	debug (very verbose)

Retrieving Library Size

Usage:

libsize LIBRARY_FILE (*.smi, *.sdf, *.mol2, *.ldb)

Retrieving Database Information

Usage:

idbinfo [Mandatory arguments] [Optional arguments]

Mandatory arguments:

--dbase, -d {file}

database to investigate (*.ldb)

Optional arguments:

--complete, -c		perform complete analysis (takes long for large databases)
--help, -h		command line parameter help
--sysinfo		system information
--log-file, -l {logfile}		output file for logging-messages (default: stdout)

Merging Databases

Usage:

idbmerger [Mandatory arguments] [Optional arguments] [LIBRARY_FILE (*.ldb) .. ]

Mandatory arguments:

--output, -o {outfile}

output file (*.ldb)

Optional arguments:

--help, -h		command line parameter help
--sysinfo		system information
--allow-duplicates, -A		allow duplicates in the database (default: off)

Retrieving Start Position File from Library

Usage:

libpos [Mandatory arguments]

Mandatory arguments:

--input, -i {infile}		input file (.sd, .sdf, .mol, .smi)
--output, -o {outfile}		output file (*.pos)

Optional arguments:

--help, -h		command line parameter help
--sysinfo		system information

Retrieving System ID

Usage:

ligandscout_sysid

LigandScout License Activation

Usage:

ligandscout_activate [Mandatory arguments] [Optional arguments]

Mandatory arguments:

--serial-number, -s {number}

serial number

Optional arguments:

--help, -h		command line parameter help
--sysinfo		system information
--license-file, -f {file}		license file
--proxy-address, -a {address}		proxy address
--proxy-port, -p {number}		proxy port
--proxy-user, -u {username}		proxy username
--proxy-password, -w {username}		proxy password

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