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タグ: correlated_mutations [39 articles]

Recent papers classified by the tag correlated_mutations.
  • Co-Evolving Motions at Protein−Protein Interfaces of Two-Component Signaling Systems Identified by Covariance Analysis
    Biochemistry (28 June 2008)
    by Hendrik Szurmant, Benjamin G Bobay, Robert A White, Daniel M Sullivan, Richele J Thompson, Terence Hwa, James A Hoch, John Cavanagh
    posted to correlated_mutations dynamics histidine-kinase kinase nmr protein signaling two-component by pansapiens on 2008-07-12 03:00:13 as ** along with 4 people raik marck neils paulschlesinger
  • Correlated mutations and residue contacts in proteins.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 309-317.
    by U Göbel, C Sander, R Schneider, A Valencia
    posted to correlated_mutations ppi by jteyra on 2008-07-10 15:58:36 as ** along with 5 people gbart analogAI dgront cjeans Lombardo_7
  • The prediction of protein contacts from multiple sequence alignments.
    Protein Eng, Vol. 9, No. 11. (November 1996), pp. 941-948.
    by DJ Thomas, G Casari, C Sander
    posted to correlated_mutations by jteyra on 2008-08-19 09:23:36 as ** along with 1 person gbart
  • Can correlated mutations in protein domain families be used for protein design?
    Brief Bioinform, Vol. 2, No. 3. (1 January 2001), pp. 279-288.
    by Sylvia B Nagl
    posted to correlated_mutations by jteyra on 2008-08-19 09:28:52 as ** along with 1 person Lombardo_7
  • Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion
    Journal of Molecular Biology, Vol. 351, No. 2. (12 August 2005), pp. 345-354.
    by Nobuyuki Ota, David A Agard
    posted to allosteric contacts correlated_motions correlated_mutations md_simulation by barry to the group Bioinformatics on 2006-01-24 18:24:55 as **** along with 3 people and 1 group pansapiens lna choonpeng structural_bioinformatics
  • In silico Discovery of Enzyme-Substrate Specificity-determining Residue Clusters
    Journal of Molecular Biology, Vol. 352, No. 5. (7 October 2005), pp. 1105-1117.
    by Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Rajesh Munavalli, Al Geist, Nagiza F Samatova
    posted to bioinf_methods correlated_mutations protein_design protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-15 18:06:44 as **** along with 1 person and 1 group cjeans structural_bioinformatics
  • Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450.
    by ME Hatley, SW Lockless, SK Gibson, AG Gilman, R Ranganathan
    posted to sca g_proteins correlated_mutations contacts by barry to the group Bioinformatics on 2007-02-05 21:58:17 as read along with 4 people and 4 groups lna Einat marcius caporaso structural_bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • A method to predict functional residues in proteins.
    Nat Struct Biol, Vol. 2, No. 2. (February 1995), pp. 171-178.
    by G Casari, C Sander, A Valencia
    posted to bioinf_methods correlated_mutations protein_design protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-16 23:37:03 as read along with 1 person and 1 group sriram_s structural_bioinformatics
  • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 211-221.
    by AA Fodor, RW Aldrich
    posted to correlated_mutations multiple_sequence_alignment protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-27 22:05:54 as *** along with 6 people and 1 group gbart cjeans jlh64 mingzhi dgront Lombardo_7 structural_bioinformatics
  • Protein co-evolution, co-adaptation and interactions
    The EMBO Journal, Vol. aop, No. current. (25 September 2008)
    by Florencio Pazos, Alfonso Valencia
    posted to review protein_protein phylogeny correlated_mutations by barry to the group Bioinformatics on 2008-10-02 20:24:17 as ***** along with 1 person and 2 groups sjcockell structural_bioinformatics McCammon
  • Correlated substitution analysis and the prediction of amino acid structural contacts
    Brief Bioinform (13 November 2007), bbm052.
    by David S Horner, Walter Pirovano, Graziano Pesole
    posted to correlated_mutations review by barry to the group Bioinformatics on 2007-11-27 23:34:46 as * along with 3 people and 2 groups zwang sobolevnrm Lombardo_7 structural_bioinformatics baker-group
  • On evolutionary conservation of thermodynamic coupling in proteins.
    J Biol Chem, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050.
    by AA Fodor, RW Aldrich
    posted to correlated_mutations protein_evolution protein_folding protein_function protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-27 22:12:45 as *** along with 7 people and 1 group barry gbart cjeans tale friendpine ca3295 Lombardo_7 structural_bioinformatics
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058., pp. 512-518.
    by Michael Socolich, Steve W Lockless, William P Russ, Heather Lee, Kevin H Gardner, Rama Ranganathan
    posted to correlated_mutations protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-22 23:02:40 as read along with 14 people and 4 groups barry lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Structural biologyForm and function instructions
    Nature, Vol. 437, No. 7058. (21 September 2005), pp. 486-487.
    by Jeffery W Kelly
    posted to correlated_mutations protein_design protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-22 23:01:12 as *** along with 2 people and 1 group barry dayjm structural_bioinformatics
  • Detection and reduction of evolutionary noise in correlated mutation analysis
    Protein Engineering, Design and Selection, Vol. 18, No. 5. (1 May 2005), pp. 247-253.
    by Orly Noivirt, Miriam Eisenstein, Amnon Horovitz
    posted to correlated_mutations sequence_comparison by barry to the group Bioinformatics on 2006-01-25 04:24:16 as ** along with 2 people and 1 group gbart cjeans structural_bioinformatics
  • Natural-like function in artificial WW domains
    Nature, Vol. 437, No. 7058., pp. 579-583.
    by William P Russ, Drew M Lowery, Prashant Mishra, Michael B Yaffe, Rama Ranganathan
    posted to correlated_mutations protein_design protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-22 23:00:20 as **** along with 6 people and 4 groups barry balajis marcius caporaso bethbromley ca3295 structural_bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 333-340.
    by SD Dunn, LM Wahl, GB Gloor
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-01-31 12:19:53 as read along with 3 people bicko zwang marck
  • Analysis of the residue-residue coevolution network and the functionally important residues in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Byung-Chul Lee, Keunwan Park, Dongsup Kim
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-03-11 11:40:31 as read along with 7 people and 1 group barry neils mingzhi penpen926 scienbox wilbur friendpine structural_bioinformatics
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-01-03 12:32:12 as read along with 11 people balicea skhadar zwang niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine pradiptaray
  • Analysis of correlated mutations in HIV-1 protease using spectral clustering
    Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1243-1250.
    by Ying Liu, Eran Eyal, Ivet Bahar
    posted to correlated_mutations quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-06-20 11:35:34 as read along with 2 people Ema bmaust
  • Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Susan Tang, Jung-Chi Liao, Alexander R Dunn, Russ B Altman, James A Spudich, Jeanette P Schmidt
    posted to correlated_mutations bioinformatics allostery by sobolevnrm to the group baker-group on 2007-09-04 12:46:29 as read along with 5 people and 1 group barry choonpeng cactus jlh64 melting structural_bioinformatics
  • The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jonathan Manning, Emily Jefferson, Geoffrey Barton
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-02-26 11:59:01 as read along with 2 people laughcry dgront
  • How Directional Translocation is Regulated in a DNA Helicase Motor
    Biophys. J. (17 August 2007), biophysj.107.109546.
    by Jin Yu, Taekjip Ha, Klaus Schulten
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc helicase correlated_mutations allostery by sobolevnrm to the group baker-group on 2007-08-26 19:58:10 as read
  • Contact rearrangements form coupled networks from local motions in allosteric proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Michael D Daily, Tarak J Upadhyaya, Jeffrey J Gray
    posted to allostery correlated_mutations molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-11-08 12:54:28 as read
  • The CHAIN program: forging evolutionary links to underlying mechanisms
    Trends in Biochemical Sciences, Vol. 32, No. 11. (November 2007), pp. 487-493.
    by Andrew F Neuwald
    posted to bioinformatics correlated_mutations software by sobolevnrm to the group baker-group on 2007-11-01 17:28:53 as read
  • Evolution of protein sequences and structures.
    J Mol Biol, Vol. 291, No. 4. (27 August 1999), pp. 977-995.
    by TC Wood, WR Pearson
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2007-12-19 12:35:44 as read along with 2 people and 2 groups ana rabio structural_bioinformatics Bioinformatics
  • An integrated system for studying residue coevolution in proteins
    Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 290-292.
    by Kevin Y Yip, Prianka Patel, Philip M Kim, Donald M Engelman, Drew Mcdermott, Mark Gerstein
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-01-14 12:28:24 as read along with 3 people chrys friendpine ca3295
  • Positional dependence, cliques, and predictive motifs in the bHLH protein domain.
    J Mol Evol, Vol. 48, No. 5. (May 1999), pp. 501-516.
    by WR Atchley, W Terhalle, A Dress
    posted to correlated_mutations by gbart on 2006-10-06 12:05:38 as **
  • A simple tool to explore the distance distribution of correlated mutations in proteins.
    Biophys Chem, Vol. 119, No. 3. (1 February 2006), pp. 240-246.
    by R Perez-Jimenez, R Godoy-Ruiz, A Parody-Morreale, B Ibarra-Molero, JM Sanchez-Ruiz
    posted to correlated_mutations by gbart on 2006-10-04 16:24:52 as ** along with 1 person Lombardo_7
  • Natural Selection for Kinetic Stability Is a Likely Origin of Correlations between Mutational Effects on Protein Energetics and Frequencies of Amino Acid Occurrences in Sequence Alignments.
    J Mol Biol, Vol. 362, No. 5. (6 October 2006), pp. 966-978.
    by R Godoy-Ruiz, F Ariza, D Rodriguez-Larrea, R Perez-Jimenez, B Ibarra-Molero, JM Sanchez-Ruiz
    posted to correlated_mutations by gbart on 2006-10-04 16:25:41 as **
  • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    Protein Eng, Vol. 7, No. 3. (March 1994), pp. 349-358.
    by IN Shindyalov, NA Kolchanov, C Sander
    posted to 3d_contacts correlated_mutations by gbart on 2006-10-04 16:22:16 as ** along with 2 people nirfriedman kieran101
  • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations.
    Proteins, Vol. 48, No. 4. (1 September 2002), pp. 611-617.
    by I Kass, A Horovitz
    posted to correlated_mutations by gbart on 2006-10-06 12:06:50 as **
  • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions.
    J Mol Biol, Vol. 303, No. 3. (27 October 2000), pp. 433-446.
    by SM Larson, AA Di Nardo, AR Davidson
    posted to correlated_mutations by gbart on 2006-10-06 12:06:15 as ** along with 6 people and 2 groups ana analogAI Haggan cjeans tale bethbromley structural_bioinformatics Bioinformatics
  • Effective use of sequence correlation and conservation in fold recognition.
    J Mol Biol, Vol. 293, No. 5. (12 November 1999), pp. 1221-1239.
    by O Olmea, B Rost, A Valencia
    posted to correlated_mutations fold_discrimination fold_recognition by gbart on 2006-10-06 12:09:49 as ** along with 1 person cjeans
  • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
    Proteins (28 February 2006)
    by Inbal Halperin, Haim Wolfson, Ruth Nussinov
    posted to correlated_mutations by gbart on 2006-10-04 16:24:06 as ** along with 7 people bicko ramensky cjeans tale mingzhi friendpine Lombardo_7
  • How frequent are correlated changes in families of protein sequences?
    Proc Natl Acad Sci U S A, Vol. 91, No. 1. (4 January 1994), pp. 98-102.
    by E Neher
    posted to correlated_mutations by gbart on 2006-10-06 12:04:55 as ** along with 2 people Haggan friendpine
  • Statistical Coupling Analysis of Aspartic Proteinases Based on Crystal Structures of the Trichoderma reesei Enzyme and Its Complex with Pepstatin A
    Journal of Molecular Biology, Vol. 382, No. 3. (10 October 2008), pp. 763-778.
    by Alessandro S Nascimento, Sandra Krauchenco, Alexander M Golubev, Alla Gustchina, Alexander Wlodawer, Igor Polikarpov
    posted to sca protein_structure protein_sequence correlated_mutations by barry on 2008-09-04 02:24:58 as **
  • Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 994-999.
    by RA Estabrook, J Luo, MM Purdy, V Sharma, P Weakliem, TC Bruice, NO Reich
    posted to correlated_motions correlated_mutations protein_design protein_dynamics protein_evolution by barry on 2005-10-26 00:16:13 as *** along with 4 people and 2 groups ana pansapiens dimka gbart structural_bioinformatics Bioinformatics
  • Local complexity of amino acid interactions in a protein core.
    Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116.
    by RK Jain, R Ranganathan
    posted to core_residues core_structure correlated_mutations protein_design protein_structure by barry on 2006-09-29 19:24:22 as ** along with 5 people and 4 groups ana lna marcius gbart choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
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