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Group: baker-group - with tag correlated_mutations [105 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag correlated_mutations
  • 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
  • Analysis of the residue-residue coevolution network and the functionally important residues in proteins
    Proteins (in press)
    by BC Lee, K Park, D Kim
    posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-05-15 11:44:28 as read
  • 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
  • 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 3 people nklee laughcry dgront
  • 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
  • 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 4 people marck chrys friendpine ca3295
  • 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
  • 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
  • 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 bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2007-11-14 11:52:21 as read along with 3 people and 2 groups barry zwang Lombardo_7 structural_bioinformatics Bioinformatics
  • 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
  • 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
  • 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
  • Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
    Bioinformatics, Vol. 23, No. 14. (2007), pp. 1837-9.
    by E Eyal, S Pietrokovski, I Bahar
    posted to software correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-08-10 13:06:00 as read
  • Specificity in protein interactions and its relationship with sequence diversity and coevolution
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by L Hakes, SC Lovell, SG Oliver, DL Robertson
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase
    Biochemistry (in press)
    by RE Amaro, A Sethi, RS Myers, VJ Davisson, Luthey Z Schulten
    posted to correlated_mutations bioinformatics allostery by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • CAPS: coevolution analysis using protein sequences
    Bioinformatics, Vol. 22, No. 22. (2006), pp. 2821-2.
    by MA Fares, D Mcnally
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type 1 Envelope Protein: An Information Theoretic Analysis
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 90, No. 15. (1993), pp. 7176-80.
    by BTM Korber, RM Farber, DH Wolpert, AS Lapedes
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Genetic correlations in mutation processes
    Physical Review E, Vol. 59, No. 6. (1999), pp. 7000-7.
    by Ben E Naim, AS Lapedes
    posted to statistical_mechanics correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Bayesian shadows of molecular mechanisms cast in the light of evolution
    Trends in Biochemical Sciences, Vol. 31, No. 7. (2006), pp. 374-82.
    by AF Neuwald
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses
    Genetics, Vol. 173, No. 1. (2006), pp. 9-23.
    by MA Fares, SAA Travers
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 20. (2006), pp. 7664-9.
    by W Zheng, BR Brooks, D Thirumalai
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlated_mutations allostery by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families
    Proteins, Vol. 63, No. 4. (2006), pp. 832-45.
    by I Halperin, H Wolfson, R Nussinov
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins
    Proteins, Vol. 63, No. 1. (2006), pp. 87-99.
    by I Mihalek, I Res, O Lichtarge
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:53 as read
  • Determination of network of residues that regulate allostery in protein families using sequence analysis
    Protein Science, Vol. 25, No. 2. (2006), pp. 258-68.
    by RI Dima, D Thirumalai
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as read
  • Inferring functional information from domain co-evolution
    Bioinformatics, Vol. 22, No. 1. (2006), pp. 40-9.
    by Y Kim, M Koyutã¼rk, U Topkara, A Grama, S Subramaniam
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as read
  • The evolutionary history of Cys-tRNACys formation
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 52. (2005), pp. 19003-8.
    by P O'Donoghue, A Sethi, CR Woese, Luthey Z Schulten
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as read
  • Species-specific analysis of protein sequence motifs using mutual information
    BMC Bioinformatics, Vol. 6 (2005)
    by J Hummel, N Keshvari, W Weckwerth, J Selbig
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as read
  • On the Evolution of Structure in Aminoacyl-tRNA Synthetases
    Microbiology and Molecular Biology Reviews, Vol. 67, No. 4. (2003), pp. 550-73.
    by P O'Donoghue, Luthey Z Schulten
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as read
  • Evolutionary profiles from the QR factorization of multiple sequence alignments
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 11. (2005), pp. 4045-50.
    by A Sethi, P O'Donoghue, Luthey Z Schulten
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as read
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058. (2005), pp. 512-8.
    by M Socolich, SW Lockless, WP Russ, H Lee, KH Gardner, R Ranganathan
    posted to protein_folding correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as read
  • STRING: known and predicted proteinâprotein associations, integrated and transferred across organisms
    Nucleic Acids Research, Vol. 33, No. S1. (2005), pp. D433-D437.
    by C von Mering, LJ Jensen, B Snel, SD Hooper, M Krupp, M Foglierini, N Jouffre, MA Huynen, P Bork
    posted to database correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as read
  • Prolinks: a database of protein functional linkages derived from coevolution
    Genome Biology, Vol. 5, No. 5. (2004)
    by PM Bowers, M Pellegrini, MJ Thompson, J Fierro, TO Yeates, D Eisenberg
    posted to database correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as read
  • A Model-Based Approach for Detecting Coevolving Positions in a Molecule
    Molecular Biology and Evolution, Vol. 22, No. 9. (2005), pp. 1919-28.
    by J Dutheil, T Pupko, Jean A Marie, N Galtier
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:25 as read
  • Structure, function, and evolution of transient and obligate proteinâprotein interactions
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 31. (2005), pp. 10930-5.
    by J Mintseris, Z Weng
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:24 as read
  • Random Matrix Analysis of Human EEG Data
    Physical Review Letters, Vol. 91, No. 19. (2003)
    by P Seba
    posted to mathematics correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:24 as read
  • Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity
    Journal of Molecular Biology, Vol. 350, No. 3. (2005), pp. 402-15.
    by M Raviscioni, P Gu, M Sattar, AJ Cooney, O Lichtarge
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:04 as read
  • Detecting coevolving amino acid sites using Bayesian mutational mapping
    Bioinformatics, Vol. 21, No. S1. (2005), pp. i126-i135.
    by MW Dimmic, MJ Hubisz, CD Bustamante, R Nielsen
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:04 as read
  • Functional genome annotation through phylogenomic mapping
    Nature Biotechnology, Vol. 23, No. 6. (2005), pp. 691-8.
    by BS Srinivasan, NB Caberoy, G Suen, RG Taylor, R Shah, F Tengra, BS Goldman, AG Garza, RD Welch
    posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Detection and reduction of evolutionary noise in correlated mutation analysis
    Protein Engineering Design and Selection, Vol. 18, No. 5. (2005), pp. 247-53.
    by O Noivirt, M Eisenstein, A Horovitz
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions
    Biochemistry, Vol. 44, No. 19. (2005), pp. 7156-65.
    by GB Gloor, LC Martin, LM Wahl, SD Dunn
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Networks of Coevolving Sites in Structural and Functional Domains of Serpin Proteins
    Molecular Biology and Evolution, Vol. 22, No. 7. (2005), pp. 1627-34.
    by MJ Buck, WR Atchley
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Detection of subunit interfacial modifications by tracing the evolution of clampâloader complex
    Protein Engineering Design and Selection, Vol. 18, No. 3. (2005), pp. 139-45.
    by M Saito, T Oyama, T Shirai
    posted to protein-protein_interactions correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Network of Dynamically Important Residues in the Open/Closed Transition in Polymerases Is Strongly Conserved
    Structure, Vol. 13, No. 4. (2005), pp. 565-77.
    by W Zheng, BR Brooks, S Doniach, D Thirumalai
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlated_mutations allostery by sobolevnrm to the group baker-group on 2007-05-25 14:17:40 as read
  • A systems biology perspective on protein structural dynamics and signal transduction
    Current Opinion in Structural Biology, Vol. 15, No. 1. (2005), pp. 23-30.
    by F Rousseau, J Schymkowitz
    posted to systems_biology protein-protein_interactions correlated_mutations allostery by sobolevnrm to the group baker-group on 2007-05-25 14:15:43 as read
  • Planetary Systems Biology
    Molecular Cell, Vol. 17, No. 4. (2005), pp. 471-2.
    by SA Benner, A Ricardo
    posted to systems_biology correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:15:43 as read
  • Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 4. (2005), pp. 994-9.
    by RA Eastbrook, J Luo, MM Purdy, V Sharma, P Weakliem, TC Bruice, NO Reich
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc molecular_dynamics correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:15:19 as read
  • Proteins associated with diseases show enhanced sequence correlation between charged residues
    Bioinformatics, Vol. 20, No. 15. (2004), pp. 2345-54.
    by RI Dima, D Thirumalai
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:13:42 as read
  • Beyond Consensus: Statistical Free Energies Reveal Hidden Interactions in the Design of a TPR Motif
    Journal of Molecular Biology, Vol. 343, No. 3. (2004), pp. 731-45.
    by TJ Magliery, L Regan
    posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:13:41 as read
  • In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 32. (2004), pp. 11646-51.
    by SY Park, BD Beel, MI Simon, AM Bilwes, BR Crane
    posted to protein-protein_interactions correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:12:48 as read
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