The World Wide Web as a graphical user interface to program macros for molecular graphics, molecular modeling, and structure-based drug design

Abstract

In this article we describe how the World Wide Web (WWW or Web) has been employed to provide access to computational chemistry software and protein structure data via program macros. We show how the combination of Web technology and macros can automate both the running of chemistry software and the execution of complex operations on protein structures. The current version of the system supports the molecular visualization packages GRASP,¹ RASMOL,² MOLVIEWER-OGL³ and INSIGHT95,⁴ and the ligand design tool GRID⁵ and includes more than 175 in-house protein-ligand complexes. The approach enables in-experienced users to confidently make full use of sophisticated modeling techniques by offering only sensible options, hiding parameter settings, and controlling program invocation and macro excution. Our interface provides both the expert and non-expert alike with powerful tools for protein structure visualization, molecular modeling, and rational drug design.