Group: baker-group - with tag correlated_mutations [113 articles] Export

Recent papers posted by members of the baker-group group with tag correlated_mutations

	Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution [My Copy] PLoS ONE, Vol. 4, No. 3. (10 March 2009), e4762. by Daniel Y. Little, Lu Chen posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2009-03-26 11:32:37 as along with 1 person min013
	Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors [My Copy] PLoS ONE, Vol. 4, No. 3. (5 March 2009), e4681. by Sarosh N. Fatakia, Stefano Costanzi, Carson C. Chow posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2009-03-25 11:36:12 as along with 1 person xdeupi
	Graphical models of protein-protein interaction specificity from correlated mutations and interaction data [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2 February 2009), pp. 911-929. by John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg posted to bioinformatics correlated_mutations protein-protein_interactions by sobolevnrm to the group baker-group on 2009-03-23 11:52:16 as along with 4 people and 1 group AliC qluo RebeccaHamer barry Orengo Group Journal Picks
	Correlated mutation analyses on super-family alignments reveal functionally important residues. [My Copy] Proteins, Vol. 76, No. 3. (15 August 2009), pp. 608-616. by Remko K. Kuipers, Henk-Jan J. Joosten, Eugene Verwiel, et al.Sjoerd Paans, Jasper Akerboom, John van der Oost, Nicole G. Leferink, Willem J. van Berkel, Gert Vriend, Peter J. Schaap posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2009-03-18 11:27:22 as along with 5 people and 2 groups mgomes qluo AliC RebeccaHamer barry Orengo Group Journal Picks Bioinformatics
	Two Separate Interfaces between the Voltage Sensor and Pore Are Required for the Function of Voltage-Dependent K+ Channels [My Copy] PLoS Biology, Vol. 7, No. 3. (1 March 2009), e47. by Seok-Yong Lee, Anirban Banerjee, Roderick Mackinnon posted to bioinformatics correlated_mutations ion_channels by sobolevnrm to the group baker-group on 2009-03-12 12:32:31 as along with 1 person tyrell_turing
	Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree [My Copy] Journal of Molecular Biology, Vol. 385, No. 1. (09 January 2009), pp. 91-98. by M. Kann, B. Shoemaker, A. Panchenko, T. Przytycka posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2009-03-12 12:31:03 as along with 11 people and 1 group mgomes biomcgary chica druvus mhofree grahamc barry zwang marti reyez paulschlesinger Bioinformatics
	Identification of direct residue contacts in protein–protein interaction by message passing [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 67-72. by Martin Weigt, Robert A. White, Hendrik Szurmant, James A. Hoch, Terence Hwa posted to allostery bioinformatics correlated_mutations structure by sobolevnrm to the group baker-group on 2009-03-05 12:34:10 as along with 6 people and 1 group orr cactus haisent sjcockell akraemer hmk KeatingJClub
	Surface Sites for Engineering Allosteric Control in Proteins [My Copy] Science, Vol. 322, No. 5900. (17 October 2008), pp. 438-442. by Jeeyeon Lee, Madhusudan Natarajan, Vishal C. Nashine, et al.Michael Socolich, Tina Vo, William P. Russ, Stephen J. Benkovic, Rama Ranganathan posted to allostery correlated_mutations by sobolevnrm to the group baker-group on 2009-01-28 13:10:50 as along with 7 people and 3 groups jbhiatt lflorez cactus marck i000 barry paulschlesinger structural_bioinformatics McCammon Bioinformatics
	Analysis of correlated mutations in HIV-1 protease using spectral clustering [My Copy] 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 along with 3 people RebeccaHamer Ema bmaust
	Analysis of the residue-residue coevolution network and the functionally important residues in proteins [My Copy] Proteins (in press) by B. C. 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
	Analysis of the residue-residue coevolution network and the functionally important residues in proteins [My Copy] 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 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 [My Copy] 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 along with 3 people nklee laughcry dgront
	Mutual Information Without the Influence of Phylogeny or Entropy Dramatically Improves Residue Contact Prediction [My Copy] Bioinformatics, Vol. 24, No. 3. (5 December 2007), pp. btm604-340. by S. D. Dunn, L. M. Wahl, G. B. Gloor posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-01-31 12:19:53 as along with 5 people mgomes qluo bicko zwang marck
	An integrated system for studying residue coevolution in proteins [My Copy] 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 along with 6 people leemond31 qluo marck chrys friendpine ca3295
	Detecting coevolution in and among protein domains. [My Copy] PLoS computational biology, Vol. 3, No. 11. (1 November 2007), e211. by Chen-Hsiang H. Yeang, David Haussler posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2008-01-03 12:32:12 as along with 12 people martainn balicea skhadar zwang niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine pradiptaray
	Evolution of protein sequences and structures. [My Copy] J Mol Biol, Vol. 291, No. 4. (27 August 1999), pp. 977-995. by T. C. Wood, W. R. Pearson posted to bioinformatics correlated_mutations by sobolevnrm to the group baker-group on 2007-12-19 12:35:44 as along with 2 people and 2 groups ana rabio structural_bioinformatics Bioinformatics
	Correlated substitution analysis and the prediction of amino acid structural contacts [My Copy] 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 along with 6 people and 2 groups mgomes qluo RebeccaHamer barry zwang Lombardo_7 structural_bioinformatics Bioinformatics
	Contact rearrangements form coupled networks from local motions in allosteric proteins [My Copy] 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
	The CHAIN program: forging evolutionary links to underlying mechanisms [My Copy] 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
	Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues [My Copy] 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 along with 5 people and 1 group barry choonpeng cactus jlh64 melting structural_bioinformatics
	How Directional Translocation is Regulated in a DNA Helicase Motor [My Copy] 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
	Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices [My Copy] 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
	Specificity in protein interactions and its relationship with sequence diversity and coevolution [My Copy] Proceedings of the National Academy of Sciences of the United States of America (in press) by L. Hakes, S. C. Lovell, S. G. Oliver, D. L. Robertson posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as
	A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase [My Copy] Biochemistry (in press) by R. E. Amaro, A. Sethi, R. S. Myers, V. J. 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
	CAPS: coevolution analysis using protein sequences [My Copy] Bioinformatics, Vol. 22, No. 22. (2006), pp. 2821-2. by M. A. Fares, D. Mcnally posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as
	Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type 1 Envelope Protein: An Information Theoretic Analysis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 90, No. 15. (1993), pp. 7176-80. by B. T. M. Korber, R. M. Farber, D. H. Wolpert, A. S. Lapedes posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	Genetic correlations in mutation processes [My Copy] Physical Review E, Vol. 59, No. 6. (1999), pp. 7000-7. by Ben E. Naim, A. S. Lapedes posted to statistical_mechanics correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	Bayesian shadows of molecular mechanisms cast in the light of evolution [My Copy] Trends in Biochemical Sciences, Vol. 31, No. 7. (2006), pp. 374-82. by A. F. Neuwald posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as
	A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses [My Copy] Genetics, Vol. 173, No. 1. (2006), pp. 9-23. by M. A. Fares, S. A. A. Travers posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as
	Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 20. (2006), pp. 7664-9. by W. Zheng, B. R. 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
	Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families [My Copy] 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
	Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins [My Copy] 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
	Determination of network of residues that regulate allostery in protein families using sequence analysis [My Copy] Protein Science, Vol. 25, No. 2. (2006), pp. 258-68. by R. I. Dima, D. Thirumalai posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as
	Inferring functional information from domain co-evolution [My Copy] 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
	The evolutionary history of Cys-tRNACys formation [My Copy] 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, C. R. Woese, Luthey Z. Schulten posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as
	Species-specific analysis of protein sequence motifs using mutual information [My Copy] 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
	On the Evolution of Structure in Aminoacyl-tRNA Synthetases [My Copy] 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
	Evolutionary profiles from the QR factorization of multiple sequence alignments [My Copy] 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
	Evolutionary information for specifying a protein fold [My Copy] Nature, Vol. 437, No. 7058. (2005), pp. 512-8. by M. Socolich, S. W. Lockless, W. P. Russ, H. Lee, K. H. Gardner, R. Ranganathan posted to protein_folding correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as
	STRING: known and predicted proteinâprotein associations, integrated and transferred across organisms [My Copy] Nucleic Acids Research, Vol. 33, No. S1. (2005), pp. D433-D437. by C. von Mering, L. J. Jensen, B. Snel, et al.S. D. Hooper, M. Krupp, M. Foglierini, N. Jouffre, M. A. Huynen, P. Bork posted to database correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as
	Prolinks: a database of protein functional linkages derived from coevolution [My Copy] Genome Biology, Vol. 5, No. 5. (2004) by P. M. Bowers, M. Pellegrini, M. J. Thompson, J. Fierro, T. O. Yeates, D. Eisenberg posted to database correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:43 as
	A Model-Based Approach for Detecting Coevolving Positions in a Molecule [My Copy] 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
	Structure, function, and evolution of transient and obligate proteinâprotein interactions [My Copy] 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
	Random Matrix Analysis of Human EEG Data [My Copy] 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
	Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity [My Copy] Journal of Molecular Biology, Vol. 350, No. 3. (2005), pp. 402-15. by M. Raviscioni, P. Gu, M. Sattar, A. J. Cooney, O. Lichtarge posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:04 as
	Detecting coevolving amino acid sites using Bayesian mutational mapping [My Copy] Bioinformatics, Vol. 21, No. S1. (2005), pp. i126-i135. by M. W. Dimmic, M. J. Hubisz, C. D. Bustamante, R. Nielsen posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:18:04 as
	Functional genome annotation through phylogenomic mapping [My Copy] Nature Biotechnology, Vol. 23, No. 6. (2005), pp. 691-8. by B. S. Srinivasan, N. B. Caberoy, G. Suen, et al.R. G. Taylor, R. Shah, F. Tengra, B. S. Goldman, A. G. Garza, R. D. Welch posted to correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as
	Detection and reduction of evolutionary noise in correlated mutation analysis [My Copy] 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
	Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions [My Copy] Biochemistry, Vol. 44, No. 19. (2005), pp. 7156-65. by G. B. Gloor, L. C. Martin, L. M. Wahl, S. D. Dunn posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as
	Networks of Coevolving Sites in Structural and Functional Domains of Serpin Proteins [My Copy] Molecular Biology and Evolution, Vol. 22, No. 7. (2005), pp. 1627-34. by M. J. Buck, W. R. Atchley posted to correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as

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bioinformatics	34
protein_sequence	24
protein_structure	22
protein_design	21
statistical_coupling_analysis	15
protein_evolution	14
allostery	11
sca	11
sequence_comparison	10
allosteric	7
bioinf_methods	7
contacts	7
protein_protein	7
review	7
correlated_motions	5
phylogeny	4
g_proteins	3
md_simulation	3
multiple_sequence_alignment	3
protein_folding	3
protein_function	3
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	3
quasiharmonic_models	3
sequence_conservation	3
structure	3
helicase	2
ion_channels	2
molecular_simulation	2
pdz	2
protein	2
protein-protein_interactions	2
software	2
3d_contacts	1
core_residues	1
core_structure	1
dynamics	1
evolution	1
fold_discrimination	1
fold_recognition	1
histidine-kinase	1
kinase	1
nmr	1
ppi	1
protein_dynamics	1
signaling	1
two-component	1

Group: baker-group - with tag correlated_mutations [113 articles] Export

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