TY - JOUR AU - Dodson, G. AU - Verma, C. S. PY - 2006 DA - 2006// TI - Protein flexibility: Its role in structure and mechanism revealed by molecular simulations JO - Cellular and Molecular Life Sciences VL - 63 UR - https://doi.org/10.1007/s00018-005-5236-7 DO - 10.1007/s00018-005-5236-7 ID - Dodson2006 ER - TY - CHAP AU - Teilum, K. AU - Olsen, J. G. AU - Kragelund, B. B. PY - 2009 DA - 2009// TI - Functional aspects of protein flexibility BT - Cellular and Molecular Life Sciences ID - Teilum2009 ER - TY - JOUR AU - Boehr, D. D. AU - Dyson, H. J. AU - Wright, P. E. PY - 2006 DA - 2006// TI - An NMR perspective on enzyme dynamics JO - Chemical Reviews VL - 106 UR - https://doi.org/10.1021/cr050312q DO - 10.1021/cr050312q ID - Boehr2006 ER - TY - JOUR AU - Henzler-Wildman, K. A. AU - Lei, M. AU - Thai, V. AU - Kerns, S. J. AU - Karplus, M. AU - Kern, D. PY - 2007 DA - 2007// TI - A hierarchy of timescales in protein dynamics is linked to enzyme catalysis JO - Nature VL - 450 UR - https://doi.org/10.1038/nature06407 DO - 10.1038/nature06407 ID - Henzler-Wildman2007 ER - TY - JOUR AU - Hammes-Schiffer, S. AU - Benkovic, S. J. PY - 2006 DA - 2006// TI - Relating protein motion to catalysis JO - Annual Review of Biochemistry VL - 75 UR - https://doi.org/10.1146/annurev.biochem.75.103004.142800 DO - 10.1146/annurev.biochem.75.103004.142800 ID - Hammes-Schiffer2006 ER - TY - JOUR AU - Smock, R. G. AU - Gierasch, L. M. PY - 2009 DA - 2009// TI - Sending signals dynamically JO - Science VL - 324 UR - https://doi.org/10.1126/science.1169377 DO - 10.1126/science.1169377 ID - Smock2009 ER - TY - JOUR AU - Ma, J. PY - 2005 DA - 2005// TI - Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes JO - Structure VL - 13 UR - https://doi.org/10.1016/j.str.2005.02.002 DO - 10.1016/j.str.2005.02.002 ID - Ma2005 ER - TY - JOUR AU - Hall, B. A. AU - Kaye, S. L. AU - Pang, A. AU - Perera, R. AU - Biggin, P. C. PY - 2007 DA - 2007// TI - Characterization of Protein Conformational States by Normal-Mode Frequencies JO - J Am Chem Soc VL - 129 UR - https://doi.org/10.1021/ja071797y DO - 10.1021/ja071797y ID - Hall2007 ER - TY - JOUR AU - Keskin, O. AU - Jernigan, R. L. AU - Bahar, I. PY - 2000 DA - 2000// TI - Proteins with similar architecture exhibit similar large-scale dynamic behaviour JO - Biophys J VL - 78 UR - https://doi.org/10.1016/S0006-3495(00)76756-7 DO - 10.1016/S0006-3495(00)76756-7 ID - Keskin2000 ER - TY - JOUR AU - Karplus, M. AU - Kuriyan, J. PY - 2005 DA - 2005// TI - Molecular dynamics and protein function JO - Proceedings of the National Academy of Sciences of the United States of America VL - 102 UR - https://doi.org/10.1073/pnas.0408930102 DO - 10.1073/pnas.0408930102 ID - Karplus2005 ER - TY - JOUR AU - Karplus, M. AU - McCammon, J. A. PY - 2002 DA - 2002// TI - Molecular dynamics simulations of biomolecules JO - Nat Struct Biol VL - 9 UR - https://doi.org/10.1038/nsb0902-646 DO - 10.1038/nsb0902-646 ID - Karplus2002 ER - TY - JOUR AU - Cox, K. AU - Sansom, M. S. P. PY - 2009 DA - 2009// TI - One membrane protein, two structures and six environments: A comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP JO - Molecular Membrane Biology VL - 26 UR - https://doi.org/10.1080/09687680902788967 DO - 10.1080/09687680902788967 ID - Cox2009 ER - TY - JOUR AU - Lama, D. AU - Sankararamakrishnan, R. PY - 2008 DA - 2008// TI - Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: Comparative molecular dynamics simulations JO - Proteins: Structure, Function and Genetics VL - 73 UR - https://doi.org/10.1002/prot.22075 DO - 10.1002/prot.22075 ID - Lama2008 ER - TY - JOUR AU - Yaneva, R. AU - Springer, S. AU - Zacharias, M. PY - 2009 DA - 2009// TI - Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study JO - Biopolymers VL - 91 UR - https://doi.org/10.1002/bip.21078 DO - 10.1002/bip.21078 ID - Yaneva2009 ER - TY - JOUR AU - Zacharias, M. AU - Springer, S. PY - 2004 DA - 2004// TI - Conformational flexibility of the MHC Class alpha1-alpha2 domain in peptide bound and free states: A molecular dynamics simulation study JO - Biophysical Journal VL - 87 UR - https://doi.org/10.1529/biophysj.104.044743 DO - 10.1529/biophysj.104.044743 ID - Zacharias2004 ER - TY - JOUR AU - Pang, A. AU - Arinaminpathy, Y. AU - Sansom, M. S. P. AU - Biggin, P. C. PY - 2005 DA - 2005// TI - Comparative Molecular Dynamics: Similar folds and similar motions? JO - Proteins: Struct Funct Bioinf VL - 61 UR - https://doi.org/10.1002/prot.20672 DO - 10.1002/prot.20672 ID - Pang2005 ER - TY - JOUR AU - Papaleo, E. AU - Riccardi, L. AU - Villa, C. AU - Fantucci, P. AU - De Gioia, L. PY - 2006 DA - 2006// TI - Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family JO - Biochimica et Biophysica Acta - Proteins and Proteomics VL - 1764 UR - https://doi.org/10.1016/j.bbapap.2006.06.005 DO - 10.1016/j.bbapap.2006.06.005 ID - Papaleo2006 ER - TY - JOUR AU - Spiwok, V. AU - Lipovová, P. AU - Skálová, T. AU - Dusková, J. AU - Dohnálek, J. AU - Hasek, J. AU - Russell, N. J. AU - Králová, B. PY - 2007 DA - 2007// TI - Cold-active enzymes studied by comparative molecular dynamics simulation JO - Journal of Molecular Modeling VL - 13 UR - https://doi.org/10.1007/s00894-006-0164-5 DO - 10.1007/s00894-006-0164-5 ID - Spiwok2007 ER - TY - JOUR AU - Maguid, S. AU - Fernandez-Alberti, S. AU - Ferrelli, L. AU - Echave, J. PY - 2005 DA - 2005// TI - Exploring the common dynamics of homologous proteins. Application to the globin family JO - Biophysical Journal VL - 89 UR - https://doi.org/10.1529/biophysj.104.053041 DO - 10.1529/biophysj.104.053041 ID - Maguid2005 ER - TY - JOUR AU - Carnevale, V. AU - Raugei, S. AU - Micheletti, C. AU - Carloni, P. PY - 2006 DA - 2006// TI - Convergent dynamics in the protease enzymatic superfamily JO - J Am Chem Soc VL - 128 UR - https://doi.org/10.1021/ja060896t DO - 10.1021/ja060896t ID - Carnevale2006 ER - TY - JOUR AU - Zen, A. AU - Carnevale, V. AU - Lesk, A. M. AU - Micheletti, C. PY - 2008 DA - 2008// TI - Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families JO - Protein Sci VL - 17 UR - https://doi.org/10.1110/ps.073390208 DO - 10.1110/ps.073390208 ID - Zen2008 ER - TY - JOUR AU - Zen, A. AU - de Chiara, C. AU - Pastore, A. AU - Micheletti, C. PY - 2009 DA - 2009// TI - Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp339 DO - 10.1093/bioinformatics/btp339 ID - Zen2009 ER - TY - JOUR AU - Fanning, A. S. AU - Anderson, J. M. PY - 1999 DA - 1999// TI - PDZ domains: Fundamental building blocks in the organization of protein complexes at the plasma membrane JO - Journal of Clinical Investigation VL - 103 UR - https://doi.org/10.1172/JCI6509 DO - 10.1172/JCI6509 ID - Fanning1999 ER - TY - JOUR AU - Van Ham, M. AU - Hendriks, W. PY - 2003 DA - 2003// TI - PDZ domains - Glue and guide JO - Molecular Biology Reports VL - 30 UR - https://doi.org/10.1023/A:1023941703493 DO - 10.1023/A:1023941703493 ID - Van Ham2003 ER - TY - JOUR AU - Harris, B. Z. AU - Lim, W. A. PY - 2001 DA - 2001// TI - Mechanism and role of PDZ domains in signaling complex assembly JO - Journal of Cell Science VL - 114 ID - Harris2001 ER - TY - JOUR AU - Jelen, F. AU - Oleksy, A. AU - Smietana, K. AU - Otlewski, J. PY - 2003 DA - 2003// TI - PDZ domains - Common players in the cell signaling JO - Acta Biochimica Polonica VL - 50 ID - Jelen2003 ER - TY - JOUR AU - Jemth, P. AU - Gianni, S. PY - 2007 DA - 2007// TI - PDZ Domains: Folding and Binding JO - Biochemistry VL - 46 UR - https://doi.org/10.1021/bi7008618 DO - 10.1021/bi7008618 ID - Jemth2007 ER - TY - JOUR AU - Hung, A. Y. AU - Sheng, M. PY - 2002 DA - 2002// TI - PDZ domains: Structural modules for protein complex assembly JO - Journal of Biological Chemistry VL - 277 UR - https://doi.org/10.1074/jbc.R100065200 DO - 10.1074/jbc.R100065200 ID - Hung2002 ER - TY - JOUR AU - Tonikian, R. AU - Zhang, Y. AU - Sazinsky, S. L. AU - Currell, B. AU - Yeh, J. -. H. AU - Reva, B. AU - Held, H. A. AU - Appleton, B. A. AU - Evangelista, M. AU - Wu, Y. PY - 2008 DA - 2008// TI - A Specificity Map for the PDZ Domain Family JO - PLoS Biol VL - 6 UR - https://doi.org/10.1371/journal.pbio.0060239 DO - 10.1371/journal.pbio.0060239 ID - Tonikian2008 ER - TY - JOUR AU - Chen, J. R. AU - Chang, B. H. AU - Allen, J. E. AU - Stiffler, M. A. AU - MacBeath, G. PY - 2008 DA - 2008// TI - Predicting PDZ domain-peptide interactions from primary sequences JO - Nature Biotechnology VL - 26 UR - https://doi.org/10.1038/nbt.1489 DO - 10.1038/nbt.1489 ID - Chen2008 ER - TY - JOUR AU - Ponting, C. P. PY - 1997 DA - 1997// TI - Evidence for PDZ domains in bacteria, yeast, and plants JO - Protein Science VL - 6 UR - https://doi.org/10.1002/pro.5560060225 DO - 10.1002/pro.5560060225 ID - Ponting1997 ER - TY - BOOK AU - De Los Rios, P. AU - Cecconi, F. AU - Pretre, A. AU - Dietler, G. AU - Michielin, O. AU - Piazza, F. PY - 2005 DA - 2005// TI - Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis. ID - De Los Rios2005 ER - TY - JOUR AU - Law, A. B. AU - Fuentes, E. J. AU - Lee, A. L. PY - 2009 DA - 2009// TI - Conservation of side-chain dynamics within a protein family JO - J Am Chem Soc VL - 131 UR - https://doi.org/10.1021/ja809915a DO - 10.1021/ja809915a ID - Law2009 ER - TY - JOUR AU - Holm, L. AU - Sander, C. PY - 1993 DA - 1993// TI - Protein structure comparison by alignment of distance matrices JO - Journal of Molecular Biology VL - 233 UR - https://doi.org/10.1006/jmbi.1993.1489 DO - 10.1006/jmbi.1993.1489 ID - Holm1993 ER - TY - JOUR AU - Aung, A. AU - Tan, K. -. L. PY - 2006 DA - 2006// TI - MatAlign: Precise protein structure comparison by matrix alignment JO - J Bioinf Comp Biol VL - 4 UR - https://doi.org/10.1142/S0219720006002417 DO - 10.1142/S0219720006002417 ID - Aung2006 ER - TY - JOUR AU - Beique, J. C. AU - Andrade, R. PY - 2003 DA - 2003// TI - PSD-95 regulates synaptic transmission and plasticity in rat cerebral cortex JO - Journal of Physiology VL - 546 UR - https://doi.org/10.1113/jphysiol.2002.031369 DO - 10.1113/jphysiol.2002.031369 ID - Beique2003 ER - TY - JOUR AU - Holm, L. AU - Park, J. PY - 2000 DA - 2000// TI - DaliLite workbench for protein structure comparison JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.6.566 DO - 10.1093/bioinformatics/16.6.566 ID - Holm2000 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: The European Molecular Biology Open Software Suite JO - Trends in Genetics VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - Liao, D. -. I. AU - Qian, J. AU - Chisholm, D. A. AU - Jordan, D. B. AU - Diner, B. A. PY - 2000 DA - 2000// TI - Crystal structures of the photosystem II D1 C-terminal processing protease JO - Nat Struc Bio VL - 7 UR - https://doi.org/10.1038/78973 DO - 10.1038/78973 ID - Liao2000 ER - TY - JOUR AU - Krojer, T. AU - Garrido-Franco, M. AU - Huber, R. AU - Ehrmann, M. AU - Clausen, T. PY - 2002 DA - 2002// TI - Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine JO - Nature VL - 416 UR - https://doi.org/10.1038/416455a DO - 10.1038/416455a ID - Krojer2002 ER - TY - JOUR AU - Wilken, C. AU - Kitzing, K. AU - Kurzbauer, R. AU - Ehrmann, M. AU - Clausen, T. PY - 2004 DA - 2004// TI - Crystal Structure of the DegS Stress Sensor: How a PDZ Domain Recognizes Misfolded Protein and Activates a Protease JO - Cell VL - 117 UR - https://doi.org/10.1016/S0092-8674(04)00454-4 DO - 10.1016/S0092-8674(04)00454-4 ID - Wilken2004 ER - TY - JOUR AU - Lindahl, E. AU - Hess, B. AU - Spoel, D. v. a. n. d. e. r. PY - 2001 DA - 2001// TI - GROMACS 3.0: A package for molecular simulation and trajectory analysis JO - J Mol Model VL - 7 ID - Lindahl2001 ER - TY - JOUR AU - Spoel, D. v. a. n. d. e. r. AU - Lindahl, E. AU - Hess, B. AU - Groenhof, G. AU - Mark, A. E. AU - Berendsen, H. J. C. PY - 2005 DA - 2005// TI - GROMACS: fast, flexible and free JO - J Comput Chem VL - 26 UR - https://doi.org/10.1002/jcc.20291 DO - 10.1002/jcc.20291 ID - Spoel2005 ER - TY - JOUR AU - Jorgensen, W. L. AU - Tirado-Rives, J. PY - 1988 DA - 1988// TI - The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin JO - J Am Chem Soc VL - 110 UR - https://doi.org/10.1021/ja00214a001 DO - 10.1021/ja00214a001 ID - Jorgensen1988 ER - TY - JOUR AU - Metropolis, N. AU - Rosenbluth, A. W. AU - Rosenbluth, M. N. AU - Teller, A. H. AU - Teller, E. PY - 1953 DA - 1953// TI - Equation of state calculations by fast computing machines JO - J Chem Phys VL - 21 UR - https://doi.org/10.1063/1.1699114 DO - 10.1063/1.1699114 ID - Metropolis1953 ER - TY - JOUR AU - Johnson, D. S. AU - Aragon, C. R. AU - McGeoch, L. A. AU - Schevon, C. PY - 1989 DA - 1989// TI - Optimization by Simulated Annealing: An Experimental Evaluation; Part I, Graph Partitioning JO - Operations Research VL - 37 UR - https://doi.org/10.1287/opre.37.6.865 DO - 10.1287/opre.37.6.865 ID - Johnson1989 ER -