10 research outputs found
Knowledge-based energy functions for computational studies of proteins
This chapter discusses theoretical framework and methods for developing
knowledge-based potential functions essential for protein structure prediction,
protein-protein interaction, and protein sequence design. We discuss in some
details about the Miyazawa-Jernigan contact statistical potential,
distance-dependent statistical potentials, as well as geometric statistical
potentials. We also describe a geometric model for developing both linear and
non-linear potential functions by optimization. Applications of knowledge-based
potential functions in protein-decoy discrimination, in protein-protein
interactions, and in protein design are then described. Several issues of
knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe
Nucleosomes in gene regulation: theoretical approaches
This work reviews current theoretical approaches of biophysics and
bioinformatics for the description of nucleosome arrangements in chromatin and
transcription factor binding to nucleosomal organized DNA. The role of
nucleosomes in gene regulation is discussed from molecular-mechanistic and
biological point of view. In addition to classical problems of this field,
actual questions of epigenetic regulation are discussed. The authors selected
for discussion what seem to be the most interesting concepts and hypotheses.
Mathematical approaches are described in a simplified language to attract
attention to the most important directions of this field
The 4D nucleome project
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells
Strategies for protein folding and design
Fundamental challenges in molecular biology can be addressed by using simple models on a lattice, where statistical mechanics and combinatoric techniques can be employed. The basic premise is that it is sensible to test any proposed method on the simplest of models in order to assess their validity before launching a full-scale attack on realistic problems. In this paper we follow this strategy and we present different efficient schemes to perform protein design and to extract effective amino acid interaction potentials