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Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein(More)
The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract A new hazard analysis technique, called System-Theoretic Process Analysis, is capable of identifying potential hazardous design flaws, including software and system design errors and unsafe interactions among multiple system(More)
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue(More)
As a genre of computer games, the massively multiplayer online game (MMOG) has the promise of enabling up to tens—or even hundreds—of thousands of simultaneous players. This paper describes how we began with an existing single-server online game engine and enhanced it to become a multiserver MMOG engine running on a grid. Other approaches require that a(More)
Protein-protein interactions are mediated by complementary amino acids defining complementary surfaces. Typically not all members of a family of related proteins interact equally well with all members of a partner family; thus analysis of the sequence record can reveal the complementary amino acid partners that confer interaction specificity. This article(More)
Computer system users today are inundated with a flood of semi-structured information, such as documents, electronic mail, programs, and images. Today, this information is typically stored in filesystems that provide limited support for organizing, searching, and operating upon this data, all operations that are vital to the ability of users to effectively(More)
In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: a b s t r a c t The methods currently used to assure the safety of planned changes to(More)
Interaction design is becoming increasingly complex and diverse. Complexity increases because existing technologies are becoming smaller and cheaper and thus more ubiquitous, even as new I/O devices are invented. This complexity is increased by the task of integrating technologies into workplaces which we are recognizing as filled with existing customs and(More)