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Janet Thornton
European Bioinformatics Institute (EBI), United Kingdom

Faculty Member: GENOMICS & GENETICS > Bioinformatics [ since 12 February 2002 ]
[ Biography ] [ Evaluations ]
Biography

Acknowledgements:
I would like to acknowledge the help Matthew Bashton provides in compiling my evaluations for Faculty of 1000.

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Evaluations

Contact patterns between helices and strands of sheet define protein folding patterns.
Kamat AP, Lesk AM
Proteins 2007 Mar 1 66(4):869-76 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 10 Apr 2008

Convergent evolution of enzyme active sites is not a rare phenomenon.
Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ
J Mol Biol 2007 Sep 21 372(3):817-45 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 25 Jan 2008

Quantification of the elevated rate of domain rearrangements in metazoa.
Ekman D, Björklund AK, Elofsson A
J Mol Biol 2007 Oct 5 372(5):1337-48 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 25 Jan 2008

Sequence patterns associated with disordered regions in proteins.
Lise S, Jones DT
Proteins 2005 Jan 1 58(1):144-50 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 20 Jan 2005

A simple physical model for the prediction and design of protein-DNA interactions.
Havranek JJ, Duarte CM, Baker D
J Mol Biol 2004 Nov 12 344(1):59-70 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 19 Nov 2004

Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites.
Basu G, Sivanesan D, Kawabata T, Go N
J Mol Biol 2004 Sep 17 342(3):1053-66 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 26 Oct 2004

Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
Kashtan N, Itzkovitz S, Milo R, Alon U
Bioinformatics 2004 Jul 22 20(11):1746-58 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 2 Sep 2004

Moment-based prediction of DNA-binding proteins.
Ahmad S, Sarai A
J Mol Biol 2004 Jul 30 341(1):65-71 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 2 Sep 2004

Modulation of agrin function by alternative splicing and Ca2+ binding.
Stetefeld J, Alexandrescu AT, …, Ruegg MA, Kammerer RA
Structure 2004 Mar 12(3):503-15 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 6 Apr 2004

Heat capacity effects of water molecules and ions at a protein-DNA interface.
Bergqvist S, Williams MA, O'Brien R, Ladbury JE
J Mol Biol 2004 Feb 27 336(4):829-42 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton / Kenneth P. Murphy
Evaluated 2 Apr 2004

Supra-domains: evolutionary units larger than single protein domains.
Vogel C, Berzuini C, …, Gough J, Teichmann SA
J Mol Biol 2004 Feb 20 336(3):809-23 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 18 Mar 2004

Conserved spatially interacting motifs of protein superfamilies: application to fold recognition and function annotation of genome data.
Bhaduri A, Ravishankar R, Sowdhamini R
Proteins 2004 Mar 1 54(4):657-70 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 17 Mar 2004

Enzyme family classification by support vector machines.
Cai CZ, Han LY, Ji ZL, Chen YZ
Proteins 2004 Apr 1 55(1):66-76 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 17 Mar 2004

TGF-beta signaling in fibroblasts modulates the oncogenic potential of adjacent epithelia.
Bhowmick NA, Chytil A, …, Neilson EG, Moses HL
Science 2004 Feb 6 303(5659):848-51 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Valeri Vasioukhin / Janet Thornton / Ulf Pettersson / Thomas Ried / Richard Pestell
Evaluated 26 Feb 2004

Structural distortion of p53 by the mutation R249S and its rescue by a designed peptide: implications for "mutant conformation".
Friedler A, DeDecker BS, …, Rüdiger S, Fersht AR
J Mol Biol 2004 Feb 6 336(1):187-96 [abstract on PubMed] [related articles] [order article]
Selected by | H Jane Dyson / Janet Thornton
Evaluated 13 Feb 2004

Structure-based active site profiles for genome analysis and functional family subclassification.
Cammer SA, Hoffman BT, …, Baxter SM, Fetrow JS
J Mol Biol 2003 Nov 28 334(3):387-401 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 30 Jan 2004

Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues.
Lamoureux JS, Maynes JT, Glover JN
J Mol Biol 2004 Jan 9 335(2):399-408 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton / Phoebe Rice
Evaluated 16 Jan 2004

Protein adaptations to temperature and pressure: complementary roles of adaptive changes in amino acid sequence and internal milieu.
Somero GN
Comp Biochem Physiol B Biochem Mol Biol 2003 Dec 136(4):577-91 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 15 Jan 2004

A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology.
Chou KC, Cai YD
Biochem Biophys Res Commun 2003 Nov 21 311(3):743-7 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 12 Jan 2004

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins.
Mao L, Wang Y, Liu Y, Hu X
J Am Chem Soc 2003 Nov 26 125(47):14216-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 12 Jan 2004

Evaluation of protein fold comparison servers.
Novotny M, Madsen D, Kleywegt GJ
Proteins 2004 Feb 1 54(2):260-70 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 9 Jan 2004

A novel database of disulfide patterns and its application to the discovery of distantly related homologs.
van Vlijmen HW, Gupta A, Narasimhan LS, Singh J
J Mol Biol 2004 Jan 23 335(4):1083-92 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 8 Jan 2004

Cupins: the most functionally diverse protein superfamily?
Dunwell JM, Purvis A, Khuri S
Phytochemistry 2004 Jan 65(1):7-17 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 8 Jan 2004

Beta-sheet preferences from first principles.
Rossmeisl J, Kristensen I, …, Jacobsen KW, Nørskov JK
J Am Chem Soc 2003 Dec 31 125(52):16383-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 8 Jan 2004

Using multiple sequence correlation analysis to characterize functionally important protein regions.
Saraf MC, Moore GL, Maranas CD
Protein Eng 2003 Jun 16(6):397-406 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 21 Nov 2003

Atomic contact vectors in protein-protein recognition.
Mintseris J, Weng Z
Proteins 2003 Nov 15 53(3):629-39 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 20 Nov 2003

Inferring functional relationships of proteins from local sequence and spatial surface patterns.
Binkowski TA, Adamian L, Liang J
J Mol Biol 2003 Sep 12 332(2):505-26 [abstract on PubMed] [related articles] [order article]
Selected by | Rob Russell / Janet Thornton
Evaluated 4 Nov 2003

Survey for g-proteins in the prokaryotic genomes: prediction of functional roles based on classification.
Pandit SB, Srinivasan N
Proteins 2003 Sep 1 52(4):585-97 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 29 Oct 2003

A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
Day R, Beck DA, Armen RS, Daggett V
Protein Sci 2003 Oct 12(10):2150-60 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton / Thomas Szyperski
Evaluated 17 Oct 2003

A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes.
Kuttner YY, Sobolev V, Raskind A, Edelman M
Proteins 2003 Aug 15 52(3):400-11 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 4 Sep 2003

Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.
Matta CF, Bader RF
Proteins 2003 Aug 15 52(3):360-99 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 4 Sep 2003

Calmodulin target database.
Yap KL, Kim J, …, Yuan T, Ikura M
J Struct Funct Genomics 2000 1(1):8-14 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 26 Aug 2003

The cadherin superfamily database.
Truong K, Ikura M
J Struct Funct Genomics 2002 2(3):135-43 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 26 Aug 2003

Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
Wang X, He X, …, Chang W, Liang D
J Bacteriol 2003 Jul 185(14):4248-55 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 8 Aug 2003

A phylogenetic approach to assessing the significance of missense mutations in disease genes.
Santibáñez Koref MF, Gangeswaran R, …, Shanahan N, Hancock JM
Hum Mutat 2003 Jul 22(1):51-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 6 Aug 2003

Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.
Koike A, Kobayashi Y, Takagi T
Genome Res 2003 Jun 13(6A):1231-43 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 6 Aug 2003

Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
Kato S, Han SY, …, Kanamaru R, Ishioka C
Proc Natl Acad Sci U S A 2003 Jul 8 100(14):8424-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 9 Jul 2003

Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families.
Rigden DJ, Jedrzejas MJ, de Mello LV
FEBS Lett 2003 Jun 5 544(1-3):103-11 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 20 Jun 2003

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
Ma B, Elkayam T, Wolfson H, Nussinov R
Proc Natl Acad Sci U S A 2003 May 13 100(10):5772-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 20 Jun 2003

Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation.
Govindarajan S, Ness JE, …, Minshull J, Gustafsson C
J Mol Biol 2003 May 16 328(5):1061-9 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 20 Jun 2003

Prediction of enzyme family classes.
Chou KC, Elrod DW
J Proteome Res 2003 Mar-Apr 2(2):183-90 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 13 Jun 2003

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.
Jensen LJ, Skovgaard M, …, Petersen N, Ussery D
BMC Genomics 2003 Apr 2 4(1):12 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 11 Jun 2003

Predicting gene function from patterns of annotation.
King OD, Foulger RE, …, White JV, Roth FP
Genome Res 2003 May 13(5):896-904 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 10 Jun 2003

Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos I, Tsoka S, …, Sander C, Ouzounis CA
Bioinformatics 2003 Apr 12 19(6):717-26 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 10 Jun 2003

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.
Ota M, Kinoshita K, Nishikawa K
J Mol Biol 2003 Apr 11 327(5):1053-64 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser / Janet Thornton
Evaluated 23 May 2003

GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, …, Giegerich R, Pühler A
Nucleic Acids Res 2003 Apr 15 31(8):2187-95 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 1 May 2003

Nonrandom tripeptide sequence distributions at protein carboxyl termini.
Gatto GJ, Berg JM
Genome Res 2003 Apr 13(4):617-23 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 1 May 2003

A novel method for finding tRNA genes.
Tsui V, Macke T, Case DA
RNA 2003 May 9(5):507-17 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 29 Apr 2003

Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains.
Cheng AC, Chen WW, Fuhrmann CN, Frankel AD
J Mol Biol 2003 Apr 4 327(4):781-96 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 28 Apr 2003

Conservation of electrostatic properties within enzyme families and superfamilies.
Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S
Biochemistry 2003 Apr 1 42(12):3464-73 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton / Antonio Rosato
Evaluated 25 Apr 2003

The Z curve database: a graphic representation of genome sequences.
Zhang CT, Zhang R, Ou HY
Bioinformatics 2003 Mar 22 19(5):593-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 24 Apr 2003

ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes.
Guo FB, Ou HY, Zhang CT
Nucleic Acids Res 2003 Mar 15 31(6):1780-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 24 Apr 2003

New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor.
Yeats C, Bentley S, Bateman A
BMC Microbiol 2003 Feb 6 3:3 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 22 Apr 2003

In silico analysis of the EPS8 gene family: genomic organization, expression profile, and protein structure.
Tocchetti A, Confalonieri S, …, Di Fiore PP, Betsholtz C
Genomics 2003 Feb 81(2):234-44 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 22 Apr 2003

The phylogenetic extent of metabolic enzymes and pathways.
Peregrin-Alvarez JM, Tsoka S, Ouzounis CA
Genome Res 2003 Mar 13(3):422-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 17 Apr 2003

The codon 72 polymorphic variants of p53 have markedly different apoptotic potential.
Dumont P, Leu JI, …, George DL, Murphy M
Nat Genet 2003 Mar 33(3):357-65 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 16 Apr 2003

Detailed computational study of p53 and p16: using evolutionary sequence analysis and disease-associated mutations to predict the functional consequences of allelic variants.
Greenblatt MS, Beaudet JG, …, Koh J, Bond JP
Oncogene 2003 Feb 27 22(8):1150-63 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Janet Thornton
Evaluated 15 Apr 2003

Efficient identification of side-chain patterns using a multidimensional index tree.
Hamelryck T
Proteins 2003 Apr 1 51(1):96-108 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser / Janet Thornton
Evaluated 15 Apr 2003

Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide.
Vicens Q, Westhof E
J Mol Biol 2003 Feb 28 326(4):1175-88 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 26 Mar 2003

An accurate, sensitive, and scalable method to identify functional sites in protein structures.
Yao H, Kristensen DM, …, Kavraki L, Lichtarge O
J Mol Biol 2003 Feb 7 326(1):255-61 [abstract on PubMed] [related articles] [order article]
Selected by | Antonio Rosato / Janet Thornton
Evaluated 19 Mar 2003

Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.
Yang JK, Park MS, Waldo GS, Suh SW
Proc Natl Acad Sci U S A 2003 Jan 21 100(2):455-60 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet Thornton
Evaluated 19 Mar 2003

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
Kortemme T, Morozov AV, Baker D
J Mol Biol 2003 Feb 28 326(4):1239-59 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 17 Mar 2003

Functional sites in protein families uncovered via an objective and automated graph theoretic approach.
Wangikar PP, Tendulkar AV, …, Mali DN, Sarawagi S
J Mol Biol 2003 Feb 21 326(3):955-78 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 17 Mar 2003

Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?
Fernández A, Kardos J, Goto Y
FEBS Lett 2003 Feb 11 536(1-3):187-92 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton
Evaluated 13 Mar 2003

Functional fingerprints of folds: evidence for correlated structure-function evolution.
Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI
J Mol Biol 2003 Feb 7 326(1):1-9 [abstract on PubMed] [related articles] [order article]
Selected by | Janet Thornton / Arcady Mushegian
Evaluated 26 Feb 2003

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms.
Ma H, Zeng AP
Bioinformatics 2003 Jan 22 19(2):270-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Janet&#