TY - JOUR AU - Wriggers, W. AU - Schulten, K. PY - 1997 DA - 1997// TI - Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates JO - Proteins: Structure, Function, and Genetics VL - 29 UR - https://doi.org/3.0.CO;2-J DO - 3.0.CO;2-J ID - Wriggers1997 ER - TY - JOUR AU - Holm, L. AU - Sander, C. PY - 1993 DA - 1993// TI - Protein structure comparison by alignment of distance matrices JO - J Mol Biol VL - 233 UR - https://doi.org/10.1006/jmbi.1993.1489 DO - 10.1006/jmbi.1993.1489 ID - Holm1993 ER - TY - JOUR AU - Subbiah, S. AU - Laurents, D. AU - Levitt, M. PY - 1993 DA - 1993// TI - Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core JO - curr biol VL - 3 UR - https://doi.org/10.1016/0960-9822(93)90255-M DO - 10.1016/0960-9822(93)90255-M ID - Subbiah1993 ER - TY - JOUR AU - Alexandrov, N. PY - 1996 DA - 1996// TI - SARFing the PDB JO - Protein Engineering VL - 50 UR - https://doi.org/10.1093/protein/9.9.727 DO - 10.1093/protein/9.9.727 ID - Alexandrov1996 ER - TY - JOUR AU - Shindyalov, I. AU - Bourn, P. PY - 1998 DA - 1998// TI - Protein structure alignment by incremental combinatorial extension (CE) of the optimal path JO - Protein Eng VL - 11 UR - https://doi.org/10.1093/protein/11.9.739 DO - 10.1093/protein/11.9.739 ID - Shindyalov1998 ER - TY - JOUR AU - Shatsky, M. AU - Nussinov, R. AU - Wolfson, H. PY - 2004 DA - 2004// TI - A method for simultaneous alignment of multiple protein structures JO - Proteins: Structure, Function, and Bioinformatics VL - 56 UR - https://doi.org/10.1002/prot.10628 DO - 10.1002/prot.10628 ID - Shatsky2004 ER - TY - JOUR AU - Yuan, X. AU - Bystroff, C. PY - 2003 DA - 2003// TI - Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti128 DO - 10.1093/bioinformatics/bti128 ID - Yuan2003 ER - TY - JOUR AU - Zhu, J. AU - Weng, Z. PY - 2005 DA - 2005// TI - FAST: A Novel Protein Structure Alignment Algorithm JO - Proteins: Structure, Function and Bioinformatics VL - 14 UR - https://doi.org/10.1110/ps.04898705 DO - 10.1110/ps.04898705 ID - Zhu2005 ER - TY - JOUR AU - Lindqvist, Y. AU - Schneider, G. PY - 1997 DA - 1997// TI - Circular permutations of natural protein sequences: structural evidence JO - Curr Opin Struct Biol VL - 7 UR - https://doi.org/10.1016/S0959-440X(97)80061-9 DO - 10.1016/S0959-440X(97)80061-9 ID - Lindqvist1997 ER - TY - JOUR AU - Milik, M. AU - Szalma, S. AU - Olszewski, K. PY - 2003 DA - 2003// TI - Common Structural Cliques: a tool for protein structure and function analysis JO - Protein Engineering VL - 16 UR - https://doi.org/10.1093/protein/gzg080 DO - 10.1093/protein/gzg080 ID - Milik2003 ER - TY - JOUR AU - Shatsky, M. AU - Nussinov, R. AU - Wolfson, H. PY - 2002 DA - 2002// TI - Flexible protein alignment and hinge detection JO - Proteins: Structure, Function, and Bioinformatics VL - 48 UR - https://doi.org/10.1002/prot.10100 DO - 10.1002/prot.10100 ID - Shatsky2002 ER - TY - JOUR AU - Ye, Y. AU - Godzik, A. PY - 2003 DA - 2003// TI - Flexible structure alignment by chaining aligned fragment pairs allowing twists JO - Bioinformatics VL - 19 ID - Ye2003 ER - TY - JOUR AU - Kolodny, R. AU - Linial, N. PY - 2004 DA - 2004// TI - Approximate protein structural alignment in polynomial time JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0404383101 DO - 10.1073/pnas.0404383101 ID - Kolodny2004 ER - TY - JOUR AU - Needleman, S. AU - Wunsch, C. 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 - Gerstein, M. AU - Levitt, M. PY - 1996 DA - 1996// TI - Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures JO - Proc Int Conf Intell Syst Mol Biol VL - 4 ID - Gerstein1996 ER - TY - JOUR AU - Orengo, C. AU - Taylor, W. PY - 1996 DA - 1996// TI - SSAP: sequential structure alignment program for protein structure comparison JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66038-8 DO - 10.1016/S0076-6879(96)66038-8 ID - Orengo1996 ER - TY - BOOK AU - Eidhammer, I. AU - Jonassen, I. AU - Taylor, W. R. PY - 2004 DA - 2004// TI - Protein Bioinformatics: An algorithmic Approach to Sequence and Structure Analysis PB - Sons Ltd CY - UK ID - Eidhammer2004 ER - TY - JOUR AU - Eidhammer, I. AU - Jonassen, I. AU - Taylor, W. PY - 2000 DA - 2000// TI - Structure comparison and structure patterns JO - J Comput Biol VL - 7 UR - https://doi.org/10.1089/106652701446152 DO - 10.1089/106652701446152 ID - Eidhammer2000 ER - TY - BOOK AU - Garey, M. AU - Johnson, D. PY - 1979 DA - 1979// TI - Computers and Intractability: A Guide to the Theory of NP-Completeness PB - W.H. Freeman CY - San Francisco, CA ID - Garey1979 ER - TY - JOUR AU - Emekli, U. AU - Schneidman-Duhovny, D. AU - Wolfson, H. AU - Nussinov, R. AU - Haliloglu, T. PY - 2008 DA - 2008// TI - HingeProt: Automated Prediction of Hinges in Protein Structures JO - Proteins VL - 70 UR - https://doi.org/10.1002/prot.21613 DO - 10.1002/prot.21613 ID - Emekli2008 ER - TY - JOUR AU - Flores, S. AU - Keating, K. AU - Painter, J. AU - Morcos, F. AU - Nguyen, K. AU - Merritt, E. AU - Kuhn, L. AU - Gerstein, M. PY - 2008 DA - 2008// TI - HingeMaster: normal mode hinge prediction approach and integration of complementary predictors JO - Proteins VL - 73 UR - https://doi.org/10.1002/prot.22060 DO - 10.1002/prot.22060 ID - Flores2008 ER - TY - JOUR AU - Kabsch, W. PY - 1976 DA - 1976// TI - A solution for the best rotation to relate two sets of vectors JO - Acta Crystallogr VL - A32 UR - https://doi.org/10.1107/S0567739476001873 DO - 10.1107/S0567739476001873 ID - Kabsch1976 ER - TY - JOUR AU - Chwartz, J. AU - Sharir, M. PY - 1987 DA - 1987// TI - Identification of partially obscured objects in two dimensions by matching of noisy characteristic curves JO - Int J Robotics Res VL - 6 UR - https://doi.org/10.1177/027836498700600203 DO - 10.1177/027836498700600203 ID - Chwartz1987 ER - TY - BOOK AU - Gusfield, D. PY - 1999 DA - 1999// TI - Algorithms on strings, trees, and sequences: Computer science and computational biology PB - Cambridge University Press CY - New York ID - Gusfield1999 ER - TY - JOUR AU - Qi, G. AU - Lee, R. AU - Hayward, S. PY - 2005 DA - 2005// TI - A comprehensive and non-redundant database of protein domain movements JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti420 DO - 10.1093/bioinformatics/bti420 ID - Qi2005 ER - TY - JOUR AU - Mayr, G. AU - Dominques, F. AU - Lackner, P. PY - 2007 DA - 2007// TI - Comparative Analysis of Protein Structure Alignments JO - BMC Structural Biol VL - 7 ID - Mayr2007 ER - TY - JOUR AU - Zemla, A. PY - 2003 DA - 2003// TI - LGA - a Method for Finding 3D Similarities in Protein Structures JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg571 DO - 10.1093/nar/gkg571 ID - Zemla2003 ER - TY - JOUR AU - Gerstein, M. AU - Krebs, W. PY - 1998 DA - 1998// TI - A database of macromolecular motions JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.18.4280 DO - 10.1093/nar/26.18.4280 ID - Gerstein1998 ER - TY - JOUR AU - Hayward, S. AU - Berendsen, H. PY - 1998 DA - 1998// TI - Systematic Analysis of Domain Motions in Proteins from Conformational Change; New Results on Citrate Synthase and T4 Lysozyme JO - Proteins, Structure, Function and Genetics VL - 30 UR - https://doi.org/3.0.CO;2-N DO - 3.0.CO;2-N ID - Hayward1998 ER -