Ludi

Contents

Release 2000, March 2000

1. Introduction

Background

2. Theory

Interaction Site Generation

Fragment Fitting

Fragment Aligning (Linking) with Partially Built Ligands

Ludi Fragment Libraries

Standard Library

Link Library

Ludi/ACD

3. Implementation

Rules Governing the Generation of Interaction Sites

H-donor and H-acceptor Rules

Hydrophobic Contacts Rules

Summary of Rules

Prioritization of the Fitted Fragments

Receptor Mode Scoring Functions

Active Analog Mode Scoring Function

Link Scoring Function

Review Table Fields

4. Command Summary

Ludi Pulldown

Parameters

Run

Load

Review

Score

Modify_Display

Default_Display

Set_Library

Library_Filter

Add_Fragment

Specifying Link Sites

Set_Protonation

Background_Job Pulldown

Setup_Bkgd_Job

Control_Bkgd_Job

Completion_Status

Kill_Bkgd_Job

Pseudo_Atom Pulldown

Define

Rename

Delete Command

List Command

5. Genfra

Generating and adding to Ludi libraries

Runtime parameters for genfra

Example

6. Methodology

Generating Novel Ligand Candidates for a Protein of Known Structure

Generating a Ligand Candidate de Novo

Modifying a Known Ligand by Replacement

Modifying a Known Ligand By Addition

Generating Ligand Candidates Based on Active Analogs

Ludi Trouble Shooting Recommendations

Using Other Software Tools in Concert with Ludi

Restrictions and Cautions

Ludi Size Limits

Ludi Fragment Bond Orders

7. Tutorials

Pilot Online Tutorials

A. References

B. Glossary

C. File Formats

Input Files--Ludi/Run background job

Ludi Fragment Library

<run_name>.ludi_pdb, fort.10

<run_name>.ludi_pdb, fort.3

<run_name>.ludi_inhib, fort. 7

<run_name>.ludi_inp

<run_name>.ludi_env

Output Files--Ludi/Run background job

fort.46

<run_name>.ludi_int_sites, fort.11

<run_name>.ludi_pseudo_protein, fort.12

<run_name>.ludi_scores, fort.47

<run_name>.ludi_sum1, fort.48

<run_name>.ludi_sum2, fort.50

<run_name>.ludi_frag_<xxx>, fort.<yyy>

<run_name>.ludi_err, fort.49

<run_name>.ludi_log

<run_name>.ludi_targ_sites, fort.8

Input Files--Ludi/Add_Fragment background job

GENFRA_RUN.pdb_entry, GENFRA_RUN.sd_entry, fort.41

GENFRA_RUN.inp

GENFRA_RUN.env

<lib_file.struct>, <lib_file.inp>

Output Files--Ludi/Add_Fragment background job

GENFRA_RUN.log

fort.3

fort.7

<lib_file.struct>, <lib_file.inp>

Input Files--Ludi/Score background job

<run_name>.ludi_receptor, fort.10

<run_name>.ludi_ligand, fort.9

Output Files--Ludi/Score background job

<run_name>.ludi_score, <run_name>.ludi_log, fort.40, <run_name>.lig_names

<run_name>.ludi_err, fort.49