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Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages
Antonio del Sol, Marcos J Araúzo-Bravo, Dolors Amoros, Ruth Nussinov
Genome Biol. 2007; 8(5): R92. Published online 2007 May 25. doi: 10.1186/gb-2007-8-5-r92
PMCID:
PMC1929157
Abstract Full Text PDF–725K Supplementary Material
 Is Cited by the Following 14 Articles in this Archive:
HotRegion: a database of predicted hot spot clusters
Engin Cukuroglu, Attila Gursoy, Ozlem Keskin
Nucleic Acids Res. 2012 January; 40(D1): D829–D833. Published online 2011 November 12. doi: 10.1093/nar/gkr929
PMCID:
PMC3245113
Abstract Full Text PDF–2.4M
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
Anshuman Dixit, Gennady M. Verkhivker
PLoS Comput Biol. 2011 October; 7(10): e1002179. Published online 2011 October 6. doi: 10.1371/journal.pcbi.1002179
PMCID:
PMC3188506
Abstract Full Text PDF–2.3M Supplementary Material
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
Anshuman Dixit, Gennady M. Verkhivker
PLoS One. 2011; 6(10): e26071. Published online 2011 October 6. doi: 10.1371/journal.pone.0026071
PMCID:
PMC3188581
Abstract Full Text PDF–914K Supplementary Material
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Peter Csermely, Robin Palotai, Ruth Nussinov
Trends Biochem Sci. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Trends Biochem Sci. 2010 October; 35(10): 539–546. Published online 2010 June 11. doi: 10.1016/j.tibs.2010.04.009
PMCID:
PMC3018770
Abstract Full Text PDF–143K
Structure-Based Predictive Models for Allosteric Hot Spots
Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell
PLoS Comput Biol. 2009 October; 5(10): e1000531. Published online 2009 October 9. doi: 10.1371/journal.pcbi.1000531
PMCID:
PMC2748687
Abstract Full Text PDF–1.0M Supplementary Material
Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters
Jouhyun Jeon, Jae-Seong Yang, Sanguk Kim
PLoS Comput Biol. 2009 October; 5(10): e1000522. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000522
PMCID:
PMC2739438
Abstract Full Text PDF–743K Supplementary Material
Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES
Hsiao-Mei Lu, Jie Liang
PLoS Comput Biol. 2009 October; 5(10): e1000526. Published online 2009 October 2. doi: 10.1371/journal.pcbi.1000526
PMCID:
PMC2741606
Abstract Full Text PDF–1.2M Supplementary Material
A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
Julie Baussand, Alessandra Carbone
PLoS Comput Biol. 2009 September; 5(9): e1000488. Published online 2009 September 4. doi: 10.1371/journal.pcbi.1000488
PMCID:
PMC2723916
Abstract Full Text PDF–1.1M Supplementary Material
Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits
R. Potestio, F. Pontiggia, C. Micheletti
Biophys J. 2009 June 17; 96(12): 4993–5002. doi: 10.1016/j.bpj.2009.03.051
PMCID:
PMC2712024
Abstract Full Text PDF–670K Supplementary Material
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks
Moitrayee Bhattacharyya, Saraswathi Vishveshwara
BMC Struct Biol. 2009; 9: 8. Published online 2009 February 25. doi: 10.1186/1472-6807-9-8
PMCID:
PMC2656534
Abstract Full Text PDF–1.4M Supplementary Material
Amino acid substitutions in the sugar kinase/hsp70/actin superfamily conserved ATPase core of E. coli glycerol kinase modulate allosteric ligand affinity but do not alter allosteric coupling
Donald W. Pettigrew
Arch Biochem Biophys. Author manuscript; available in PMC 2010 January 15.
Published in final edited form as: Arch Biochem Biophys. 2009 January 15; 481(2): 151–156. Published online 2008 November 27. doi: 10.1016/j.abb.2008.11.020
PMCID:
PMC2660850
Abstract Full Text PDF–1.2M Supplementary Material
Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms
Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Lio', Tom L. Blundell
PLoS Comput Biol. 2008 July; 4(7): e1000135. Published online 2008 July 25. doi: 10.1371/journal.pcbi.1000135
PMCID:
PMC2447880
Abstract Full Text PDF–707K Supplementary Material
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
Arun Krishnan, Alessandro Giuliani, Joseph P. Zbilut, Masaru Tomita
PLoS ONE. 2008; 3(5): e2149. Published online 2008 May 14. doi: 10.1371/journal.pone.0002149
PMCID:
PMC2364640
Abstract Full Text PDF–458K
The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
Antonio del Sol, Pablo Carbonell
PLoS Comput Biol. 2007 December; 3(12): e239. Prepublished online 2007 October 18. Published online 2007 December 7. doi: 10.1371/journal.pcbi.0030239
PMCID:
PMC2134966
Abstract Full Text PDF–547K Supplementary Material
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