Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure

References

• Go , N. and Scherage , H. 1970 . Ring closure and local conformational deformations of chain molecules . Macromolecules , 3 : 178 – 187 .
   Google Scholar
• Wakana , H. , Wako , H. and Saito , N. 1984 . Monte-Carlo study on local and small-amplitude conformational fluctuation in hen egg-white lysozyme . Int. J. Pept. Protein Res. , 23 : 315 – 323 .
   PubMedGoogle Scholar
• Knapp , E.W. 1992 . Long-time dynamics of a polymer with rigid body monomer units relating to a protein model – comparison with the rouse model . J. Comput. Chem. , 13 : 793 – 798 .
   Web of Science ®Google Scholar
• Dodd , L.R. , Boone , T.D. and Theodorou , D.N. 1993 . A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses . Mol. Phys. , 78 : 961 – 996 .
   Web of Science ®Google Scholar
• Knapp , E.W. and Irgensdefregger , A. 1993 . Off-lattice Monte-Carlo method with constraints – Long-time dynamics of a protein model without nonbonded interactions . J. Comput. Chem. , 14 : 19 – 29 .
   Web of Science ®Google Scholar
• Coutsias , E.A. , Seok , C. , Jacobson , M.P. and Dill , K.A. 2004 . A kinematic view of loop closure . J. Comput. Chem. , 25 : 510 – 528 .
   PubMed Web of Science ®Google Scholar
• Bruccoleri , R.E. and Karplus , M. 1985 . Chain closure with bond angle variations . Macromolecules , 18 : 2767 – 2773 .
   Web of Science ®Google Scholar
• Sartori , F. , Melchers , B. , Bottcher , H. and Knapp , E.W. 1998 . An energy function for dynamics simulations of polypeptides in torsion angle space . J. Chem. Phys. , 108 : 8264 – 8276 .
   Web of Science ®Google Scholar
• Deem , M.W. and Bader , J.S. 1996 . A configurational bias Monte Carlo method for linear and cyclic peptides . Mol. Phys. , 87 : 1245 – 1260 .
   Web of Science ®Google Scholar
• Dinner , A.R. 2000 . Local deformations of polymers with nonplanar rigid main-chain internal coordinates . J. Comput. Chem. , 21 : 1132 – 1144 .
   Web of Science ®Google Scholar
• Favrin , G. , Irback , A. and Sjunnesson , F. 2001 . Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space . J. Chem. Phys. , 114 : 8154 – 8158 .
   Web of Science ®Google Scholar
• Ulmschneider , J.P. and Jorgensen , W.L. 2003 . Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias . J. Chem. Phys. , 118 : 4261 – 4271 .
   Web of Science ®Google Scholar
• Ulmschneider , J.P. and Jorgensen , W.L. 2004 . Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation . J. Am. Chem. Soc. , 126 : 1849 – 1857 .
   PubMed Web of Science ®Google Scholar
• Ulmschneider , J.O. and Jorgensen , W.L. 2004 . Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles . J. Phys. Chem. B , 108 : 16883 – 16892 .
   Web of Science ®Google Scholar
• Ulmschneider , J.P. , Ulmschneider , M.B. and Di Nola , A. 2006 . Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations . J. Phys. Chem. B , 110 : 16733 – 16742 .
   PubMed Web of Science ®Google Scholar
• Mak , C.H. , Chung , W.-Y. and Markivskiy , N.D. 2010 . RNA conformational sampling: II. Arbitrary-length multi-nucleotide loop closure . J. Chem. Theo. Comput. , in press
   Web of Science ®Google Scholar
• Mak , C.H. 2008 . RNA conformational sampling: 1. Single-nucleotide loop closure . J. Comput. Chem. , 29 : 926 – 933 .
   PubMed Web of Science ®Google Scholar
• Wedemeyer , W.J. and Scheraga , H.A. 1999 . Exact analytical loop closure in proteins using polynomial equations . J. Comput. Chem. , 20 : 819 – 844 .
   Web of Science ®Google Scholar
• Hunt , K.H. 1978 . Kinematic Geometry of Mechanisms Oxford University Press, USA
   Google Scholar
• Duffy , J. 1980 . Analysis of Mechanisms and Robot Manipulators , New York : Wiley .
   Google Scholar
• Kraulis , P.J. 1991 . MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures . J. Appl. Crystallogr. , 24 : 946 – 950 .
   Web of Science ®Google Scholar
• Chung , W.Y. 2005 . Mobility analysis of RSSR mechanisms by working volume . Trans. ASME , 127 : 156 – 159 .
   Web of Science ®Google Scholar
• Glassner , A.S. 1990 . Graphics Gems , San Diego, CA : Academic Press .
   Google Scholar
• Press , W.H. , Flannery , B.P. , Teukolsky , S.A. and Vetterling , W.T. 1992 . Numerical Recipes , Cambridge : New York .
   Google Scholar
• Ponder , J.W. and Richards , F.M. 1987 . An efficient Newton-like method for molecular mechanics energy minimization of large molecules . J. Comput. Chem. , 8 : 1016 – 1024 .
   Web of Science ®Google Scholar
• J.W. Ponder, Tinker Version 5.1, available at http://dasher.wustl.edu/tinker
   Google Scholar
• Forster , A.C. and Symons , R.H. 1987 . Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites . Cell , 49 : 211 – 220 .
   PubMed Web of Science ®Google Scholar
• Pley , H.W. , Flaherty , K.M. and McKay , D.B. 1994 . 3-dimensional structure of a hammerhead ribozyme . Nature , 372 : 68 – 74 .
   PubMed Web of Science ®Google Scholar
• Scott , W.G. , Finch , J.T. and Klug , A. 1995 . The crystal structure of an all-RNA hammerhead ribozyme – a proposed mechanism for RNA catalytic cleavage . Cell , 81 : 991 – 1002 .
   PubMed Web of Science ®Google Scholar
• Lambert , D. and Burke , J.M. 2008 . Ribozymes and RNA Catalysis , Edited by: Lilley , D.M.J. and Eckstein , F. London : Royal Society of Chemistry .
   Google Scholar
• Scott , W.G. 2008 . Ribozymes and RNA Catalysis , Edited by: Lilley , D.M.J. and Eckstein , F. London : Royal Society of Chemistry .
   Google Scholar
• Tinoco , I. and Bustamante , C. 1999 . How RNA folds . J. Mol. Biol. , 293 : 271 – 281 .
   PubMed Web of Science ®Google Scholar
• Crothers , D.M. 2000 . RNA folding pathways . Curr. Protocols Nucleic Acid Chem , 11 : 11 – 15 .
   Google Scholar
• Woodson , S.A. and Rangan , P. 2008 . Ribozymes and RNA Catalysis , Edited by: Lilley , D.M.J. and Eckstein , F. London : Royal Society of Chemistry .
   Google Scholar
• Martick , M. and Scott , W.G. 2006 . Tertiary contacts distant from the active site prime a ribozyme for catalysis . Cell , 126 : 309 – 320 .
   PubMed Web of Science ®Google Scholar
• Humphrey , W. , Dalke , A. and Schulten , K. 1996 . VMD – visual molecular dynamics . J. Mol. Graph. , 14 : 33 – 38 .
   PubMed Web of Science ®Google Scholar
• Penedo , J.C. , Wilson , T.J. , Jayasena , S.D. , Khvorova , A. and Lilley , D.M. 2004 . Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements . RNA , 10 : 880 – 888 .
   PubMed Web of Science ®Google Scholar
• Thirumalai , D. , Lee , N. , Woodson , S.A. and Klimov , D.K. 2001 . Early events in RNA folding . Annu. Rev. Phys. Chem. , 52 : 751 – 761 .
   PubMed Web of Science ®Google Scholar
• Hyeon , C. and Thirumalai , D. 2005 . Mechanical unfolding of RNA hairpins . Proc. Natl Acad. Sci. USA , 102 : 6789 – 6794 .
   PubMed Web of Science ®Google Scholar
• Cheatham , T.E. III , Cieplak , P. and Kollman , P.A. 1999 . A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat . J. Biomol. Struct. Dyn. , 16 : 845 – 862 .
   PubMed Web of Science ®Google Scholar
• Qiu , D. , Shenkin , P.S. , Hollinger , F.P. and Still , W.C. 1997 . The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate radii . J. Phys. Chem. A , 101 : 3005 – 3014 .
   Web of Science ®Google Scholar
• Hammann , C. and Lilley , D.M. 2002 . Folding and activity of the hammerhead ribozyme . Chembiochem , 3 : 690 – 700 .
   PubMedGoogle Scholar
• Bassi , G.S. , Murchie , A.I. , Walter , F. , Clegg , R.M. and Lilley , D.M. 1997 . Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study . EMBO J. , 16 : 7481 – 7489 .
   PubMed Web of Science ®Google Scholar