Proteomic Tools for the Analysis of Cytoskeleton Proteins.
Proteomic analyses have become an essential part of the toolkit of the molecular biologist, given the widespread availability of genomic data and open source or freely accessible bioinformatics software. Tools are available for detecting homologous sequences, recognizing functional domains, and modeling the three-dimensional structure for any given protein sequence. Although a wealth of structural and functional information is available for a large number of cytoskeletal proteins, with representatives spanning all of the major subfamilies, the majority of cytoskeletal proteins remain partially or totally uncharacterized. Moreover, bioinformatics tools provide a means for studying the effects of synthetic mutations or naturally occurring variants of these cytoskeletal proteins. This chapter discusses various freely available proteomic analysis tools, with a focus on in silico prediction of protein structure and function. The selected tools are notable for providing an easily accessible interface for the novice, while retaining advanced functionality for more experienced computational biologists.
Biology Program, The Graduate Center, City University of New York, New York, NY, USA.
Michael
M
Scarpati
Biochemistry Program, The Graduate Center, City University of New York, New York, NY, USA.
Mary Ellen
ME
Heavner
Biology Program, The Graduate Center, City University of New York, New York, NY, USA.
Eliza
E
Wiech
Biochemistry Program, The Graduate Center, City University of New York, New York, NY, USA. Ssingh@brooklyn.cuny.edu.|Department of Biology, Brooklyn College, City University of New York, 209 Ingersoll Hall Extension, 2900 Bedford Ave., Brooklyn, NY, 11210, USA. Ssingh@brooklyn.cuny.edu.|Biology Program, The Graduate Center, City University of New York, New York, NY, USA. Ssingh@brooklyn.cuny.edu.
Shaneen
S
Singh
D000465:Algorithms; D020816:Amino Acid Motifs; D003598:Cytoskeletal Proteins / Q000737:chemistry / Q000378:metabolism*; D030562:Databases, Protein; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment
D003598:Cytoskeletal Proteins
Comparative modeling; Homology modeling; Multiple sequence alignment; Protein domains; Proteomics; Secondary structure prediction; Sequence similarity; Structure analysis; Threading