Related Experiment Video
Updated: Mar 3, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for
Brian Kolb1,2, Levi C Lentz1, Alexie M Kolpak3
1Massachusetts Institute of Technology, Mechanical Engineering, Cambridge, MA, 02139, USA.
Abstract:
Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. The result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. This work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet's ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.
Related Concept Videos
Protein and Protein Structure
A protein's shape is critical to its function. For example, an enzyme...
Maxwell-Boltzmann Distribution: Problem Solving
This distribution function f(v) is defined by saying that the expected number N (v1,v2) of particles with speeds between v1 and v2 is given by
Structure-Activity Relationships and Drug Design
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
Protein and Protein Structures
Predicting Molecular Geometry
Structural Protein Function
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...

