Simulating Protein Motions with Rigidity Analysis

A multi-directional rapidly exploring random graph (mRRG) for protein folding

“…Here we study the performance of mRRG under different input parameters and compare against T-RRT [13] and PRM [35]. For each method, we construct a graph rooted at the native state.…”

“…PRMs were the first robotics-based algorithms applied to model protein folding [30]. The application to proteins was further refined in [36] to use rigidity information to sample conformations in a more physically realistic way.…”

“…We compare mRRG to T-RRT [13] and rigidity sampling based PRM [35] and show that the exploration with multiple directions gives better coverage than T-RRT and is comparable to PRM for all of the proteins studied. The computational requirements are also comparable to T-RRT.…”

An Interfacial Thermodynamics Model for Protein Stability

“…Instead, excluded volume effects due to van der Waals interactions are included in geometrical simulation that allows rigid clusters to wiggle about without violating any distance constraint, or without atoms passing through one another. FRODA (Framework Rigidity Optimized Dynamics Algorithm) is one method [Wells, et al 2005;Farrell, et al 2010], among others [Lei, et al 2004;Thomas, et al 2007;Jimenez-Roldan, et al 2011;Yao, et al 2012] that uses FIRST to identify a native RCD that is preserved during the simulation. FRODA efficiently explores the native state ensemble of conformations [Jacobs, 2010;David & Jacobs 2011].…”

Structural Improvement Filtering Strategy for PRM

“…In the traditional application of robotics, a valid path is defined as a collision-free path. Many of the techniques originally designed for robotics have been extended to other applications such as the study of protein folding in Biology and Chemistry [3], [5], [21]- [23], virtual prototyping in manufacturing and mechanical design [4], [8], and the simulation of characters for animation and games [13], [14].…”