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Protein function frequently involves conformational changes with largeamplitude on timescales which are difficult and computationally expensive toaccess using molecular dynamics. In this paper, we report on the combination ofthree computationally inexpensive simulation methods-normal mode analysis usingthe elastic network model, rigidity analysis using the pebble game algorithm,and geometric simulation of protein motion-to explore conformational changealong normal mode eigenvectors. Using a combination of ELNEMO and FIRST/FRODAsoftware, large-amplitude motions in proteins with hundreds or thousands ofresidues can be rapidly explored within minutes using desktop computingresources. We apply the method to a representative set of six proteins coveringa range of sizes and structural characteristics and show that the methodidentifies specific types of motion in each case and determines their amplitudelimits.

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses