Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability.
暂无分享,去创建一个
Narayanaswamy Srinivasan | Ramanathan Sowdhamini | Nagasuma Chandra | Sankaran Sandhya | Richa Mudgal | N. Chandra | R. Sowdhamini | N. Srinivasan | S. Sandhya | R. Mudgal
[1] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[2] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[3] N Srinivasan,et al. Assessment of a Rigorous Transitive Profile Based Search Method to Detect Remotely Similar Proteins , 2005, Journal of biomolecular structure & dynamics.
[4] Sean R. Eddy,et al. Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..
[5] A. Biegert,et al. Sequence context-specific profiles for homology searching , 2009, Proceedings of the National Academy of Sciences.
[6] Shashi B. Pandit,et al. SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes , 2002, Nucleic Acids Res..
[7] Michael Levitt,et al. Evolutionarily consistent families in SCOP: sequence, structure and function , 2012, BMC Structural Biology.
[8] N Srinivasan,et al. Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. , 2012, Molecular bioSystems.
[9] N. Grishin,et al. Reconstruction of ancestral protein sequences and its applications , 2004, BMC Evolutionary Biology.
[10] A. Lesk,et al. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.
[11] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[12] C. Sander,et al. The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.
[13] P. Bork,et al. Predicting functions from protein sequences—where are the bottlenecks? , 1998, Nature Genetics.
[14] S. L. Mayo,et al. De novo protein design: fully automated sequence selection. , 1997, Science.
[15] N Srinivasan,et al. Strategies for the effective identification of remotely related sequences in multiple PSSM search approach , 2007, Proteins.
[16] C A Orengo,et al. Combining sensitive database searches with multiple intermediates to detect distant homologues. , 1999, Protein engineering.
[17] L. Aravind,et al. The many faces of the helix-turn-helix domain : Transcription regulation and beyond q , 2005 .
[18] Michael Kuperberg,et al. Markov Models , 2017, Arch. Formal Proofs.
[19] Patrice Koehl,et al. ASTRAL compendium enhancements , 2002, Nucleic Acids Res..
[20] Oruganty Krishnadev,et al. MulPSSM: a database of multiple position-specific scoring matrices of protein domain families , 2005, Nucleic Acids Res..
[21] S. Balaji,et al. SUPFAM: A database of sequence superfamilies of protein domains , 2004, BMC Bioinformatics.
[22] Sean R. Eddy,et al. Hidden Markov model speed heuristic and iterative HMM search procedure , 2010, BMC Bioinformatics.
[23] David A. Lee,et al. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures , 2012, Nucleic Acids Res..
[24] Dan S. Tawfik,et al. Mutational effects and the evolution of new protein functions , 2010, Nature Reviews Genetics.
[25] C. Sander,et al. Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.
[26] Najeeb M. Halabi,et al. Protein Sectors: Evolutionary Units of Three-Dimensional Structure , 2009, Cell.
[27] David T. Jones,et al. pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination , 2009, Bioinform..
[28] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[29] S. Eddy. Hidden Markov models. , 1996, Current opinion in structural biology.
[30] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[31] D R Flower,et al. The lipocalin protein family: structural and sequence overview. , 2000, Biochimica et biophysica acta.
[32] Oruganty Krishnadev,et al. AlignHUSH: Alignment of HMMs using structure and hydrophobicity information , 2011, BMC Bioinformatics.
[33] Kimmen Sjölander,et al. COACH : profile-profile alignment of protein families using hidden Markov models , 2003 .
[34] L. Aravind,et al. Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold , 2007, Biology Direct.
[35] Peter B. McGarvey,et al. UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..
[36] Lenore Cowen,et al. Augmented training of hidden Markov models to recognize remote homologs via simulated evolution , 2009, Bioinform..
[37] V. Agrawal,et al. OB-fold: growing bigger with functional consistency. , 2003, Current protein & peptide science.
[38] L. Holm,et al. Unification of protein families. , 1998, Current opinion in structural biology.
[39] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[40] W. P. Russ,et al. Evolutionary information for specifying a protein fold , 2005, Nature.
[41] C. Chothia,et al. Intermediate sequences increase the detection of homology between sequences. , 1997, Journal of molecular biology.
[42] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[43] Nick V Grishin,et al. Using protein design for homology detection and active site searches , 2003, Proceedings of the National Academy of Sciences of the United States of America.