FSSA: a novel method for identifying functional signatures from structural alignments

FSSA: a novel method for identifying functional signatures from structural alignments (2005)

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by Kai Wang , Ram Samudrala

Venue:	Bioinformatics
Citations:	10 - 2 self

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@ARTICLE{Wang05fssa:a,
    author = {Kai Wang and Ram Samudrala},
    title = {FSSA: a novel method for identifying functional signatures from structural alignments},
    journal = {Bioinformatics},
    year = {2005},
    volume = {21},
    pages = {2969--2977}
}

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Abstract

doi:10.1093/bioinformatics/bti471

Citations

1891	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - Altschul, Madden, et al. - 1997
960	T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res - Thompson, Higgins, et al. - 1994
703	SCOP: a Structural Classification Of Proteins database for the investigation of sequences and structures - Murzin, Brenner, et al. - 1995
592	Improved tools for biological sequence comparison - Pearson, Lipman - 1988
517	SR: Profile hidden Markov models - Eddy - 1998
436	Hidden Markov models in computational biology. Applications to protein modeling - Krogh, Brown, et al. - 1994
362	Protein structure alignment by incremental combinatorial extension (CE) of the optimal path - Shindyalov, Bourne - 1998
132	Protein structure alignment - Taylor, Orengo - 1989
116	Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships - Liao, Noble - 2003
65	Protein homology detection using string alignment kernels - Saigo, Vert, et al. - 2004
63	PRINTS and its automatic supplement, preprints - Attwood, Bradley, et al. - 2003
58	Increased coverage of protein families with the blocks database servers. Nucleic Acids Res - Henikoff, Greene, et al. - 2000
58	Analysis of protein–protein interaction sites using surface patches - Jones, JM - 1997
56	MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison - Ortiz, Strauss, et al. - 2002
52	Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels - Russell, Barton - 1992
52	Evolution of function in protein superfamilies, from a structural perspective - Todd, Orengo, et al. - 2001
48	Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins - Bateman, Birney, et al. - 1999
46	D: Remote homology detection: a motif based approach - Ben-Hur, Brutlag
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
38	predictions in CASP5: Successes, failures, and prospects for complete automation - Bradley, Chivian, et al.
29	Protein clefts in molecular recognition and function - Laskowski, Luscombe, et al. - 1996
27	MASS: multiple structural alignment by secondary structures - Dror, Benyamini, et al. - 2003
27	MJ: Automated prediction of protein function and detection of functional sites from structure - Pazos, Sternberg
26	Analysis and prediction of functional sub-types from protein sequence alignments - Hannenhalli, Russell - 2000
25	Recognition of spatial motifs in protein structures - Kleywegt - 1999
24	Protein folds and families: sequence and structure alignments - Holm, Sander - 1999
23	Three-dimensional structure analysis of PROSITE patterns - Kasuya, Thornton - 1999
21	A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization - Guda, Scheeff, et al. - 2001
21	One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions - Nagano, Orengo, et al. - 2002
20	Automated multiple structure alignment and detection of a common substructural motif - Leibowitz, Fligelman, et al.
20	The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res - Orengo, Pearl, et al. - 1999
19	Supersites within superfolds. Binding site similarity in the absence of homology - Russell, Sasieni, et al. - 1998
18	Efficient remote homology detection using local structure - Hou, Hsu, et al. - 2003
18	Determination of protein function, evolution and interactions by structural genomics - Teichmann, Murzin, et al. - 2001
17	Structure motif discovery and mining the PDB - Jonassen, Eidhammer, et al.
16	An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis - Barker, Thornton - 2003
15	Structural genomics: computational methods for structure analysis - Goldsmith-Fischman, Honig - 2003
14	Elber R: Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins - Kedem, LP - 1999
12	Discovery of local packing motifs in protein structures - Jonassen, Eidhammer, et al. - 1999
12	Annotation in three dimensions. pints: Patterns in non-homologous tertiary structures - Stark, Russell
11	From structure to function: Approaches and limitations - Thornton, Todd, et al. - 2000
10	Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases - Al-Lazikani, FB, et al.
9	H.: Global mapping of the protein structure space and application in structure-based inference of protein function - Hou, Jun, et al. - 2005
9	PROTINFO: new algorithms for enhanced protein structure predictions - Hung, Ngan, et al. - 2005
7	Finding functional sites in structural genomics proteins - Stark, Shkumatov, et al. - 2004
6	Enhanced functional annotation of protein sequences via the use of structural descriptors - Gennaro - 2001
6	2003)Using structural motif templates to identify proteins with DNA binding function - Jones, Barker, et al.
6	Identification of homologous core structures - Matsuo, Bryant - 1999
5	A new bioinformatic approach to detect common 3D sites in protein structures - Jambon - 2003
5	N: ATP binding proteins with different folds share a common ATP-binding structural motif. Nat Struct Biol - Kobayashi, Go - 1997