ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.
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Arend Sidow | Kalpana Karra | Jonathan Binkley | A. Sidow | Andrew W. Kirby | E. Stone | J. Binkley | K. Karra | M. Hosobuchi | Andrew Kirby | Eric A Stone | Eric A. Stone | Midori Hosobuchi
[1] Katsuhiko Murakami,et al. Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees , 2007, Nucleic Acids Res..
[2] Jitendra Malik,et al. Normalized cuts and image segmentation , 1997, Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition.
[3] L. Pauling,et al. Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.
[4] Claudia Neuhauser,et al. The Pattern of Amino Acid Replacements in α/β-Barrels , 2002 .
[5] Claudia Neuhauser,et al. The pattern of amino acid replacements in alpha/beta-barrels. , 2002, Molecular biology and evolution.
[6] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[7] Tal Pupko,et al. A structural EM algorithm for phylogenetic inference , 2001, J. Comput. Biol..
[8] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[9] H. Kröger,et al. [Protein synthesis]. , 1974, Fortschritte der Medizin.
[10] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[11] M. Lewis,et al. A closer view of the conformation of the Lac repressor bound to operator , 2000, Nature Structural Biology.
[12] A. Zamyatnin,et al. Protein volume in solution. , 1972, Progress in biophysics and molecular biology.
[13] E. Fraenkel,et al. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. , 1999, Genes & development.
[14] A Wlodawer,et al. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.
[15] D. Eisenberg,et al. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.
[16] Arend Sidow,et al. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. , 2005, Annual review of genomics and human genetics.
[17] S. Bouvier,et al. Systematic mutation of bacteriophage T4 lysozyme. , 1991, Journal of molecular biology.
[18] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[19] A. Sidow,et al. The integrity of a cholesterol-binding pocket in Niemann–Pick C2 protein is necessary to control lysosome cholesterol levels , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[20] Christophe Dessimoz,et al. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..
[21] Justin C. Fay,et al. Sequence divergence, functional constraint, and selection in protein evolution. , 2003, Annual review of genomics and human genetics.
[22] Christian E. V. Storm,et al. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.
[23] Duncan P. Brown,et al. Functional Classification Using Phylogenomic Inference , 2006, PLoS Comput. Biol..
[24] K. Holsinger. The neutral theory of molecular evolution , 2004 .
[25] A. Sidow,et al. Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[26] W. Fitch. Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.
[27] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[28] T. Boggon,et al. C-Cadherin Ectodomain Structure and Implications for Cell Adhesion Mechanisms , 2002, Science.
[29] Itay Mayrose,et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures , 2005, Nucleic Acids Res..
[30] C. Harris,et al. The IARC TP53 database: New online mutation analysis and recommendations to users , 2002, Human mutation.
[31] A. Sidow,et al. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. , 2005, Genome research.
[32] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[33] Steven Henikoff,et al. SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..
[34] Arend Sidow,et al. Sequence First. Ask Questions Later. , 2002, Cell.
[35] Chuong B. Do,et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.
[36] P. Jeffrey,et al. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. , 1994, Science.
[37] S. Pietrokovski. Searching databases of conserved sequence regions by aligning protein multiple-alignments. , 1996, Nucleic acids research.
[38] M. Philippova,et al. Structure and Functions of Classical Cadherins , 2001, Biochemistry (Moscow).
[39] Arend Sidow,et al. Constructing a meaningful evolutionary average at the phylogenetic center of mass , 2007, BMC Bioinformatics.
[40] R Montesano,et al. Database of p53 gene somatic mutations in human tumors and cell lines. , 1994, Nucleic acids research.
[41] Gaston H. Gonnet,et al. OMA Browser - Exploring orthologous relations across 352 complete genomes , 2007, Bioinform..
[42] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[43] Jeffrey Miller,et al. Genetic Studies of Lac Repressor: 4000 Single Amino Acid Substitutions and Analysis of the Resulting Phenotypes on the Basis of the Protein Structure , 1996, German Conference on Bioinformatics.
[44] A. Sidow,et al. Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members , 2008, BMC Evolutionary Biology.
[45] S. Henikoff,et al. Predicting the effects of amino acid substitutions on protein function. , 2006, Annual review of genomics and human genetics.
[46] J H Miller,et al. Genetic studies of the lac repressor. I. Correlation of mutational sites with specific amino acid residues: construction of a colinear gene-protein map. , 1977, Journal of molecular biology.
[47] F. Cohen,et al. An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.
[48] C. Sander,et al. Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.
[49] T. Steitz,et al. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. , 1986, Annual review of biophysics and biophysical chemistry.
[50] A. Sidow,et al. Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins. , 2006, Chemistry & biology.
[51] J. Hanley,et al. The meaning and use of the area under a receiver operating characteristic (ROC) curve. , 1982, Radiology.
[52] M. Blumenkranz,et al. A novel His158Arg mutation in TIMP3 causes a late-onset form of Sorsby fundus dystrophy. , 2006, American journal of ophthalmology.
[53] Narmada Thanki,et al. CDD: specific functional annotation with the Conserved Domain Database , 2008, Nucleic Acids Res..
[54] J. Lilien,et al. Alterations in CDH15 and KIRREL3 in patients with mild to severe intellectual disability. , 2008, American journal of human genetics.
[55] D. Lipman,et al. A genomic perspective on protein families. , 1997, Science.
[56] B. Matthews,et al. A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. , 1993, Science.
[57] S. Hirohashi,et al. Molecular Cloning and Characterization of a Novel Human Classic Cadherin Homologous with Mouse Muscle Cadherin* , 1998, The Journal of Biological Chemistry.
[58] C Cruz,et al. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. , 1994, Journal of molecular biology.
[59] M. Ruggero,et al. Similarity of Traveling-Wave Delays in the Hearing Organs of Humans and Other Tetrapods , 2007, Journal for the Association for Research in Otolaryngology.
[60] Leonid Peshkin,et al. Roundup: a multi-genome repository of orthologs and evolutionary distances , 2006, Bioinform..
[61] Kara Dolinski,et al. The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists , 2007, PloS one.
[62] Piero Fariselli,et al. ConSeq: the identification of functionally and structurally important residues in protein sequences , 2004, Bioinform..
[63] Marianne Manchester,et al. Complete mutagenesis of the HIV-1 protease , 1989, Nature.
[64] N. Ben-Tal,et al. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. , 2004, Molecular biology and evolution.
[65] M. Perutz,et al. The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. , 1984, Journal of molecular biology.
[66] P. Bork,et al. Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.
[67] F. Crick. On protein synthesis. , 1958, Symposia of the Society for Experimental Biology.
[68] W. Fitch,et al. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution , 1970, Biochemical Genetics.
[69] Arend Sidow,et al. Inference of functional regions in proteins by quantification of evolutionary constraints , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[70] N. Ben-Tal,et al. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.
[71] Andreas Prlic,et al. Ensembl 2008 , 2007, Nucleic Acids Res..