Building alternate protein structures using the elastic network model
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[1] William H. Press,et al. Numerical Recipes in Fortran 77 , 1992 .
[2] D. Baker,et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.
[3] J Kuriyan,et al. Rigid protein motion as a model for crystallographic temperature factors. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[4] Florence Tama,et al. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. , 2002, Journal of molecular biology.
[5] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[6] Guang Song,et al. An enhanced elastic network model to represent the motions of domain‐swapped proteins , 2006, Proteins.
[7] Mark Gerstein,et al. Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool , 2005, Protein science : a publication of the Protein Society.
[8] M. Gerstein,et al. Conformational changes associated with protein-protein interactions. , 2004, Current opinion in structural biology.
[9] Robert L. Jernigan,et al. Dynamics of large proteins through hierarchical levels of coarse‐grained structures , 2002, J. Comput. Chem..
[10] Lars Malmström,et al. Automated prediction of CASP‐5 structures using the Robetta server , 2003, Proteins.
[11] Gregory A Voth,et al. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. , 2007, Biophysical journal.
[12] A Caflisch,et al. Computer simulations of protein folding by targeted molecular dynamics , 2000, Proteins.
[13] Mark Gerstein,et al. MolMovDB: analysis and visualization of conformational change and structural flexibility , 2003, Nucleic Acids Res..
[14] Ivet Bahar,et al. Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data , 2004, Proteins.
[15] J R Desjarlais,et al. Side-chain and backbone flexibility in protein core design. , 1999, Journal of molecular biology.
[16] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[17] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[18] Robert L Jernigan,et al. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. , 2005, Biophysical journal.
[19] Y. Sanejouand,et al. Conformational change of proteins arising from normal mode calculations. , 2001, Protein engineering.
[20] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[21] James R. Apgar,et al. Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. , 2007, Journal of molecular biology.
[22] Adrian A Canutescu,et al. A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.
[23] G. Phillips,et al. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. , 2006, Biophysical journal.
[24] A. Sali,et al. Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.
[25] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[26] G. Hummer,et al. Protein conformational transitions explored by mixed elastic network models , 2007, Proteins.
[27] T. Siméon,et al. An NMA‐guided path planning approach for computing large‐amplitude conformational changes in proteins , 2007, Proteins.
[28] P E Bourne,et al. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.
[29] William H. Press,et al. Numerical Recipes: FORTRAN , 1988 .
[30] Zheng Yuan,et al. Prediction of protein B‐factor profiles , 2005, Proteins.
[31] C. Brooks,et al. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism , 2007, Proceedings of the National Academy of Sciences.
[32] 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.
[33] M. Delarue,et al. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. , 2002, Journal of molecular biology.
[34] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[35] David E. Kim,et al. Physically realistic homology models built with ROSETTA can be more accurate than their templates. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[36] G. Phillips,et al. Dynamics of proteins in crystals: comparison of experiment with simple models. , 2002, Biophysical journal.
[37] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[38] Christopher T. Saunders,et al. Recapitulation of protein family divergence using flexible backbone protein design. , 2005, Journal of molecular biology.
[39] G. Chirikjian,et al. Efficient generation of feasible pathways for protein conformational transitions. , 2002, Biophysical journal.
[40] Guang Song,et al. How well can we understand large-scale protein motions using normal modes of elastic network models? , 2007, Biophysical journal.
[41] Martin Karplus,et al. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. , 2005, Journal of molecular biology.