Exploration of the relationship between topology and designability of conformations

Thumbnail Image
Leelananda, Sumudu
Towfic, Fadi
Kloczkowski, Andrzej
Major Professor
Committee Member
Journal Title
Journal ISSN
Volume Title
Jernigan, Robert
Distinguished Professor
Research Projects
Organizational Units
Organizational Unit
Computer Science

Computer Science—the theory, representation, processing, communication and use of information—is fundamentally transforming every aspect of human endeavor. The Department of Computer Science at Iowa State University advances computational and information sciences through; 1. educational and research programs within and beyond the university; 2. active engagement to help define national and international research, and 3. educational agendas, and sustained commitment to graduating leaders for academia, industry and government.

The Computer Science Department was officially established in 1969, with Robert Stewart serving as the founding Department Chair. Faculty were composed of joint appointments with Mathematics, Statistics, and Electrical Engineering. In 1969, the building which now houses the Computer Science department, then simply called the Computer Science building, was completed. Later it was named Atanasoff Hall. Throughout the 1980s to present, the department expanded and developed its teaching and research agendas to cover many areas of computing.

Dates of Existence

Related Units

Organizational Unit
Journal Issue
Is Version Of
Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.


This article is published as Leelananda, Sumudu P., Fadi Towfic, Robert L. Jernigan, and Andrzej Kloczkowski. "Exploration of the relationship between topology and designability of conformations." The Journal of chemical physics 134, 235101 (2011). doi: 10.1063/1.3596947. Posted with permission.

Sat Jan 01 00:00:00 UTC 2011