MCSS

Contents

Release 98.0, December 1998


MSI MCSS is based on Harvard MCSS, v2.1. Portions of this document are taken from the manual for the Harvard version by E. Evensen, D. Joseph-McCarthy and M. Karplus.

1. Introduction to MCSS

Structure-based ligand design

Ligand development

De novo ligand design

Scoring and synthetic accessibility

Multiple Copy Simulation Search (MCSS)

MCSS task flow

2. Using MCSS

Accessing MCSS

Identifying the active site

Changing MCSS parameters

Selecting functional groups

Viewing the initial distribution of groups in the active volume

Setting the MCSS host

Running MCSS

Analyzing MCSS results

Importing and displaying results files

Functional group clustering

Picking groups

3. Preparing a Macromolecule

Converting a Protein Data Bank file for MCSS

Building hydrogens

A. References

B. Functional Groups

Functional group list

Creating a new group

The group description file

Non-covalently-connected groups

C. Standalone MCSS

General description

FORTRAN programs

Working with MCSS

To run a job

To analyze the results

Test case

Example: minimizing ACAM groups in a sphere

Example: minimizing ACAM groups in a box

MCSS input file

Iteration profile file

The CHARMm string file