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SUMMARY Protein-protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking(More)
The biophysical study of protein-protein interactions and docking has important implications in our understanding of most complex cellular signaling processes. Most computational approaches to protein docking involve a tradeoff between the level of detail incorporated into the model and computational power required to properly handle that level of detail.(More)
We present an evaluation of the results of our ZDOCK and RDOCK algorithms in Rounds 3, 4, and 5 of the protein docking challenge CAPRI. ZDOCK is a Fast Fourier Transform (FFT)-based, initial-stage rigid-body docking algorithm, and RDOCK is an energy minimization algorithm for refining and reranking ZDOCK results. Of the 9 targets for which we submitted(More)
We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets(More)
UNLABELLED CaGE is a Cardiac Gene Expression knowledgebase we have developed to facilitate the analysis of genes important to human cardiac function. CaGE integrates the functionality of the LocusLink database with data from several human cardiac expression libraries, phenotypic data from OMIM and data from large-scale microarray gene expression studies to(More)
Convergence to equilibrium is an essential requirement for molecular simulation output to be accurate and reproducible. Yet testing for convergence is challenging, especially in instances where kinetic trapping and the consequent plateauing of ensemble quantities can falsely suggest premature equilibrium. Here we introduce a quantitative method for(More)
Protein-protein docking is the computational prediction of protein complex structure given the individually solved component protein structures. It is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modeling protein complex structures. Here, we report an overview of(More)
Proteins often undergo conformational changes when binding to each other. A major fraction of backbone conformational changes involves motion on the protein surface, particularly in loops. Accounting for the motion of protein surface loops represents a challenge for protein-protein docking algorithms. A first step in addressing this challenge is to(More)
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