Packing regularities in biological structures relate to their dynamics.
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[1] O. Ptitsyn,et al. Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? , 1998, Journal of molecular biology.
[2] J. Frank,et al. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[3] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[4] M. Delarue,et al. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. , 2002, Journal of molecular biology.
[5] Jianpeng Ma,et al. Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. , 2003, Journal of molecular biology.
[6] Robert L. Jernigan,et al. Important Fluctuation Dynamics of Large Protein Structures Are Preserved upon Coarse-Grained Renormalization ∗ , 2002 .
[7] K-L Ting,et al. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence , 2002, Proteins.
[8] T. Earnest,et al. Crystal Structure of the Ribosome at 5.5 Å Resolution , 2001, Science.
[9] G. Chirikjian,et al. Elastic models of conformational transitions in macromolecules. , 2002, Journal of molecular graphics & modelling.
[10] K. Hinsen. Analysis of domain motions by approximate normal mode calculations , 1998, Proteins.
[11] Joachim Frank,et al. A ratchet-like inter-subunit reorganization of the ribosome during translocation , 2000, Nature.
[12] Jianpeng Ma,et al. Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model. , 2003, Journal of molecular biology.
[13] S. Rackovsky,et al. Optimally informative backbone structural propensities in proteins , 2002, Proteins.
[14] H. Scheraga,et al. Structural Studies of Ribonuclease. V. Reversible Change of Configuration1-3 , 1961 .
[15] Patrice Koehl,et al. Protein topology and stability define the space of allowed sequences , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[16] Ivet Bahar,et al. Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data , 2004, Proteins.
[17] Robert L Jernigan,et al. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. , 2005, Biophysical journal.
[18] K A Dill,et al. Are proteins well-packed? , 2001, Biophysical journal.
[19] Sebastian Doniach,et al. A comparative study of motor-protein motions by using a simple elastic-network model , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[20] Hubert M. James,et al. Statistical Thermodynamics of Rubber Elasticity , 1953 .
[21] D. ben-Avraham,et al. Dynamic and elastic properties of F-actin: a normal-modes analysis. , 1995, Biophysical journal.
[22] R. Jernigan,et al. Residue coordination in proteins conforms to the closest packing of spheres , 2002 .
[23] G. Chirikjian,et al. An elastic network model of HK97 capsid maturation. , 2003, Journal of structural biology.
[24] K. Hinsen,et al. Analysis of domain motions in large proteins , 1999, Proteins.
[25] R. Jernigan,et al. Residue packing in proteins: Uniform distribution on a coarse-grained scale , 2002 .
[26] O. Ptitsyn,et al. Non-functional conserved residues in globins and their possible role as a folding nucleus. , 1999, Journal of molecular biology.
[27] Y. Sanejouand,et al. Hinge‐bending motion in citrate synthase arising from normal mode calculations , 1995, Proteins.
[28] Ivet Bahar,et al. Inhibitor binding alters the directions of domain motions in HIV‐1 reverse transcriptase , 2002, Proteins.
[29] Hubert M. James,et al. Theory of the Elastic Properties of Rubber , 1943 .
[30] F. Richards. Protein stability: still an unsolved problem , 1997, Cellular and Molecular Life Sciences CMLS.
[31] A. Atilgan,et al. Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability , 1998 .
[32] Gregory S Chirikjian,et al. Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA. , 2005, Journal of molecular graphics & modelling.
[33] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[34] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[35] M. Karplus,et al. The allosteric mechanism of yeast chorismate mutase: a dynamic analysis. , 2006, Journal of molecular biology.
[36] Vasant Honavar,et al. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods , 2004, BMC Bioinformatics.
[37] P. Flory,et al. Statistical thermodynamics of random networks , 1976, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.
[38] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[39] R L Jernigan,et al. Protein sequence entropy is closely related to packing density and hydrophobicity. , 2005, Protein engineering, design & selection : PEDS.
[40] R L Jernigan,et al. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. , 1999, Journal of molecular biology.
[41] S. Bryant,et al. An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.
[42] R L Jernigan,et al. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. , 1998, Journal of molecular biology.
[43] H. James,et al. Theory of the Increase in Rigidity of Rubber during Cure , 1947 .
[44] R L Jernigan,et al. Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step , 2000, Journal of biomolecular structure & dynamics.
[45] L A Mirny,et al. How evolution makes proteins fold quickly. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[46] K. Hinsen,et al. A simplified force field for describing vibrational protein dynamics over the whole frequency range , 1999 .
[47] Robert L. Jernigan,et al. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions , 2004 .
[48] Jianpeng Ma,et al. Domain movements in human fatty acid synthase by quantized elastic deformational model , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[49] Ruxandra I. Dima,et al. Asymmetry in the shapes of folded and denatured states of proteins , 2003, q-bio/0310023.
[50] Hubert M. James,et al. Elastic and Thermoelastic Properties of Rubber like Materials , 1941 .
[51] I. Bahar,et al. Gaussian Dynamics of Folded Proteins , 1997 .
[52] Y. Sanejouand. Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding. , 1996, Protein engineering.
[53] R. Jernigan,et al. Proteins with similar architecture exhibit similar large-scale dynamic behavior. , 2000, Biophysical journal.
[54] Qiang Cui,et al. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase. , 2004, Biophysical journal.
[55] Vijay S Pande,et al. Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles , 2002, Protein science : a publication of the Protein Society.
[56] Robert L Jernigan,et al. Functional motions can be extracted from on‐lattice construction of protein structures , 2003, Proteins.
[57] C. Vonrhein,et al. Structure of the 30S ribosomal subunit , 2000, Nature.
[58] Eugene I. Shakhnovich,et al. Natural selection of more designable folds: A mechanism for thermophilic adaptation , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[59] Konrad Hinsen,et al. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. , 2005, Biophysical journal.
[60] The nature of the low-frequency normal modes of the E1Ca form of the SERCA1 Ca2+-ATPase. , 2003, Annals of the New York Academy of Sciences.
[61] Robert L. Jernigan,et al. Identifying a Folding Nucleus for the Lysozyme/α-Lactalbumin Family from Sequence Conservation Clusters , 2002, Journal of Molecular Evolution.
[62] D. T. Jones. Protein structure prediction in the postgenomic era. , 2000, Current opinion in structural biology.
[63] W. Wriggers,et al. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. , 2002, Journal of molecular biology.
[64] R L Jernigan,et al. Molecular mechanisms of chaperonin GroEL-GroES function. , 2002, Biochemistry.
[65] N S Wingreen,et al. Are protein folds atypical? , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[66] Nicolas E. Buchler,et al. Effect of alphabet size and foldability requirements on protein structure designability , 1999, Proteins.
[67] R. Jernigan,et al. Global ribosome motions revealed with elastic network model. , 2004, Journal of structural biology.
[68] R. Jernigan,et al. Identification of kinetically hot residues in proteins , 1998, Protein science : a publication of the Protein Society.
[69] S. L. Mayo,et al. De novo protein design: fully automated sequence selection. , 1997, Science.
[70] H. James,et al. Simple presentation of network theory of rubber, with a discussion of other theories , 1949 .
[71] Taner Z Sen,et al. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. , 2006, Journal of chemical theory and computation.
[72] Amos Maritan,et al. Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures. , 2002, Journal of molecular biology.
[73] M. Gerstein,et al. Average core structures and variability measures for protein families: application to the immunoglobulins. , 1995, Journal of molecular biology.
[74] Designability of lattice model heteropolymers. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.
[75] Ivet Bahar,et al. DYNAMICS OF PROTEINS AND BIOMOLECULAR COMPLEXES: INFERRING FUNCTIONAL MOTIONS FROM STRUCTURE , 1999 .
[76] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[77] Robert L. Jernigan,et al. Dynamics of large proteins through hierarchical levels of coarse‐grained structures , 2002, J. Comput. Chem..
[78] F. Tama,et al. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. , 2004, Journal of molecular biology.
[79] M. Levitt,et al. Exploring conformational space with a simple lattice model for protein structure. , 1994, Journal of molecular biology.
[80] Andrzej Kloczkowski,et al. Chain dimensions and fluctuations in random elastomeric networks. 1. Phantom Gaussian networks in the undeformed state , 1989 .
[81] G. Chirikjian,et al. Efficient generation of feasible pathways for protein conformational transitions. , 2002, Biophysical journal.
[82] S. Altschul,et al. Issues in searching molecular sequence databases , 1994, Nature Genetics.
[83] Robert L Jernigan,et al. Myosin flexibility: Structural domains and collective vibrations , 2004, Proteins.
[84] Adam W Van Wynsberghe,et al. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. , 2004, Biochemistry.
[85] Robert L Jernigan,et al. Molecular mechanism of domain swapping in proteins: an analysis of slower motions. , 2004, Biophysical journal.
[86] Andrzej Kloczkowski,et al. The origin and extent of coarse‐grained regularities in protein internal packing , 2003, Proteins.
[87] Wenjun Zheng,et al. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. , 2005, Journal of molecular biology.
[88] Joachim Frank,et al. Visualization of Trna Movements on the Escherichia coli 70s Ribosome during the Elongation Cycle , 2000, The Journal of cell biology.
[89] Y. Sanejouand,et al. Dynamical properties of the MscL of Escherichia coli: a normal mode analysis. , 2003, Journal of molecular biology.
[90] H. James,et al. Theory of the Elasticity of Rubber , 1944 .
[91] Ozlem Keskin,et al. Relating molecular flexibility to function: a case study of tubulin. , 2002, Biophysical journal.
[92] D. Covell,et al. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. , 1998, Biochemistry.
[93] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[94] B. Matthews,et al. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. , 1992, Science.
[95] P. Privalov,et al. Intermediate states in protein folding. , 1996, Journal of molecular biology.
[96] C T Shih,et al. Mean-field HP model, designability and alpha-helices in protein structures. , 2000, Physical review letters.
[97] D. Ming,et al. How to describe protein motion without amino acid sequence and atomic coordinates , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[98] R L Jernigan,et al. Cooperative fluctuations and subunit communication in tryptophan synthase. , 1999, Biochemistry.
[99] C. Brooks,et al. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. , 2005, Journal of molecular biology.