Annotating nucleic acid-binding function based on protein structure

Annotating nucleic acid-binding function based on protein structure (2003)

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by Eric W. Stawiski , Lydia M. Gregoret , Yael M

Venue:	J. Mol. Biol
Citations:	13 - 0 self

BibTeX

@ARTICLE{Stawiski03annotatingnucleic,
    author = {Eric W. Stawiski and Lydia M. Gregoret and Yael M},
    title = {Annotating nucleic acid-binding function based on protein structure},
    journal = {J. Mol. Biol},
    year = {2003},
    volume = {326},
    pages = {1065--1079}
}

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Abstract

Structural genomics promises to deliver threedimensional structures of proteins on a genomic scale. 1 Since the primary goal of this initiative is to obtain structural information about proteins for

Citations

1923	Basic local alignment search tool - Altschul, Gish, et al. - 1990
1891	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - Altschul, Madden, et al. - 1997
671	Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features - Kabsch, Sander - 1983
176	BW: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta - Matthews - 1975
172	Richards F: The interpretation of protein structures: estimation of static accessibility - Lee - 1971
155	C: Enlarged representative set of protein structures. Protein Sci 1994, 3:522-24 [http://bioinfo.tg.fh-gies sen.de/pdbselect/]. Page 11 of 12 (page number not for citation purposes) Bioinformatics 2007 - Hobohm, Sander
133	An evolutionary trace method defines binding surfaces common to protein families - Lichtarge, Bourne, et al. - 1996
110	The PROSITE database; its status in - Hofmann, Bucher, et al. - 1999
83	The relationship between protein structure and function: A comprehensive survey with application to the yeast genome - Hegyi, Gerstein - 1999
64	Sequence and structure-based prediction of eukaryotic protein phosphorylation sites - Blom, Gammeltoft, et al. - 1999
58	Analysis of protein–protein interaction sites using surface patches - Jones, JM - 1997
55	JM: TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci - AC, Borkakoti, et al. - 1997
50	The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids - Berman, Olson, et al. - 1992
48	The OPLS potential function for proteins: Energy minimizations for crystals of cyclic peptides and crambin - Jorgensen, Tirado-Rives - 1657
43	Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases - Fetrow, Skolnick - 1998
40	Protein–RNA interactions: a structural analysis - Jones, Daley, et al. - 2001
39	Transcription factors: structural families and principles of DNA recognition - Pabo, Sauer - 1992
38	100,000 protein structures for the biologist. Nat Struct Biol 5 - Sali - 1998
36	Lichtarge O: Structural clusters of evolutionary trace residues are statistically significant and common in proteins - Madabushi, Yao, et al.
32	Satisfying hydrogen bonding potential in proteins - McDonald, Thornton - 1994
29	Consurf: an algorithmic tool for the identification of functional regions by surface mapping of phylogenetic information - Armon, Graur, et al. - 2001
29	Protein clefts in molecular recognition and function - Laskowski, Luscombe, et al. - 1996
29	Evolutionary predictions of binding surfaces and interactions - Lichtarge, Sowa - 2002
28	Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases - Wallace, Laskowski, et al. - 1996
28	The MIDAS display system - Ferrin, Huang, et al. - 1988
27	Threedimensional cluster analysis identifies interfaces and functional residue clusters in proteins - Landgraf, Xenarios, et al. - 2001
27	An overview of the structures of protein-DNA complexes - Luscombe, Austin, et al. - 2000
25	Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles - Mandel-Gutfreund, Schueler, et al. - 1995
22	Completeness in structural genomics - Vitkup, Melamud, et al. - 2001
22	SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions - Laskowski - 1995
19	Electrostatic aspects of protein–protein interactions - Sheinerman, Norel, et al. - 2000
17	Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci 3 - ZS, Tidor - 1994
17	Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity - Luscombe, Thornton - 2002
16	THEMATICS: a simple computational predictor of enzyme function from structure - Ondrechen, Clifton, et al. - 2001
16	Geometric analysis and comparison of protein–DNA interfaces: why is there no simple code for recognition - Pabo, Nekludova - 2000
15	GRASP: Graphical representation and analysis of surface properties - Nicholls, Bharadawaj, et al. - 1993
15	Structural features of protein-nucleic acid recognition sites - Nadassy, Wodak, et al. - 1999
15	JA: Generalized linear models 2nd edition - PM, Nelder - 1989
12	R (2000) A fast method to predict protein interaction sites from sequences - Gallet, Charloteaux, et al.
12	A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules - Suzuki - 1994
10	A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites. Acta Cryst - Gerstein - 1992
9	Prediction and confirmation of a site critical for effector regulation of RGS domain activity - Sowa - 2001
9	Predicting protein function from structure: Unique structural features of proteases - Stawiski, Baucom, et al. - 2000
8	Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily - Fetrow, Siew, et al. - 1999
7	Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct superfamilies - Gerlt, Babbitt
5	Fractal surfaces of proteins - Lewis, Rees - 1985
4	A role for CH...O interactions in protein-DNA recognition - Mandel-Gutfreund, Margalit, et al. - 1998
4	Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS. Biochemistry - Arbuzova, Wang, et al. - 2000
3	Characterization of novel proteins based on known protein structures - Koppensteiner, Lackner, et al. - 2000
3	Electrostatics and flexibility in protein-DNA interactions - Ohlendorf, Matthew - 1985