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mtw's library [207 articles]

Recent papers added to mtw's library.
  • The dispersion metric and the CMA evolution strategy
    Vol. 1 (August-December July 2006), pp. 477-484.
    by Monte Lunacek, Darrell Whitley
    edited by Maarten Keijzer, Mike Cattolico, Dirk Arnold, Vladan Babovic, Christian Blum, Peter Bosman, Martin V Butz, Carlos Coello, Dipankar Dasgupta, Sevan G Ficici, James Foster, Arturo H Aguirre, Greg Hornby, Hod Lipson, Phil Mcminn, Jason Moore, Guenther Raidl, Franz Rothlauf, Conor Ryan, Dirk Thierens
    posted to landscapes by mtw on 2006-11-09 09:46:19 as **
  • On finding all suboptimal foldings of an RNA molecule
    Science, Vol. 244 (1989), pp. 48-52.
    by M Zuker
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • RNA secondary structures and their prediction
    Bull.\ Math.\ Biol., Vol. 46 (1984), pp. 591-621.
    by M Zuker, D Sankoff
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information
    Nucl.\ Acids\ Res., Vol. 9 (1981), pp. 133-148.
    by M Zuker, P Stiegler
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Critical exponents from field theory
    Phys.\ Rev.\ B, Vol. 21, No. 9. (1980), pp. 3976-3998.
    by Zinn J Justin, JC Le Guilliou
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Monte Carlo simulation studies of the correlation between global size and helical structure in biopolymers
    J.\ Chem.\ Phys., Vol. 115, No. 13. (2001), pp. 6236-6242.
    by G Zifferer, M Hofstetter, OF Olaj
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Design of artificial short-chained RNA species that are replicated by Q$β$ replicase.
    Biochemistry, Vol. 34 (1995), pp. 1261-1266.
    by H Zamora, R Luce, CK Biebricher
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Forces of tertiary structural organization in globular proteins
    Proc.\ Natl.\ Acad.\ Sci.\ USA, Vol. 92 (1995), pp. 146-150.
    by K Yue, KA Dill
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • Complete suboptimal folding of RNA and the stability of secondary structure.
    Biopolymers, Vol. 49 (1998), pp. 145-165.
    by S Wuchty, W Fontana, IL Hofacker, P Schuster
    posted to bibtex-import by mtw on 2006-09-05 20:11:46 as **
  • RNA folding causes secondary structure rearrangement
    Biochemistry, Vol. 95 (1998), pp. 11555-11560.
    by M Wu, Tinoco
    posted to bibtex-import by mtw on 2006-09-05 20:11:45 as **
  • Efficient computation of RNA folding dynamics
    J.\ Phys.\ A:\ Math.\ Gen., Vol. 37 (2004), pp. 4731-4741.
    by MT Wolfinger, Svrcek WA Seiler, Ch, IL Hofacker, PF Stadler
    posted to bibtex-import by mtw on 2006-09-05 20:11:45 as **
  • The Energy Landscape of RNA Folding
    (2001)
    by MT Wolfinger
    posted to bibtex-import by mtw on 2006-09-05 20:11:45 as **
  • Thiamine derivatives bin messenger RNA directly to regulate bacterial gene expression
    Nature, Vol. 419 (2002), pp. 952-956.
    by W Winkler, A Nahvi, RR Breaker
    posted to bibtex-import by mtw on 2006-09-05 20:11:45 as **
  • RNA pseudoknots
    Current Opinion Struct.\ Biol., Vol. 2 (1992), pp. 327-333.
    by E Westhof, L Jaeger
    posted to bibtex-import by mtw on 2006-09-05 20:11:45 as **
  • Hsp70 and Hsp90 - a relay team for protein folding
    Rev.\ Physiol.\ Biochem.\ Pharmacol., Vol. 151 (2004), pp. 1-44.
    by H Wegele, L Müller, J Bruckner
    posted to bibtex-import by mtw on 2006-09-05 20:11:44 as **
  • RNA secondary structure: A complete mathematical analysis
    Math.\ Biosc., Vol. 42 (1978), pp. 257-266.
    by MS Waterman, TF Smith
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Co-axial stacking of helixes enhances binding of oligoribonucleotides and improves predicions of RNA folding
    Proc.\ Natl.\ Acad.\ Sci.\ USA, Vol. 91 (1994), pp. 9218-9222.
    by AE Walter, DH Turner, J Kim, MH Lyttle, P Müller, DH Mathews, M Zuker
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Archetypal energy landscapes
    Nature, Vol. 394 (1998), pp. 758-760.
    by DJ Wales, MA Miller, TR Walsh
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Vienna RNA Package
    (1994-2004)
    by IL Hofacker, W Fontana, PF Stadler, P Schuster
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Genetic algorithms for protein folding simulations
    J.\ Mol.\ Biol., Vol. 231 (1993), pp. 75-81.
    by R Unger, J Moult
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Finding lowest free energy conformation of a protein is an NP-hard problem: Proof and implications
    Bull.\ Math.\ Biol., Vol. 55 (1993), pp. 1183-1198.
    by R Unger, J Moult
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • A Dynamical Approach to Protein Folding
    J.\ Biol.\ Phys., Vol. 27 (2001), pp. 181-203.
    by A Torcini, R Livi, A Politi
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • How RNA folds
    J.\ Mol.\ Biol., Vol. 293 (1999), pp. 271-281.
    by Tinoco, C Bustamante
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Conserved RNA Secondary structures in flaviviridae genomes
    J.\ Gen.\ Virol,, Vol. 85 (2004), pp. 1113-1124.
    by C Thurner, C Witwer, IL Hofacker, PF Stadler
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Early events in RNA folding
    Annu.\ Rev.\ Phys.\ Chem., Vol. 52 (2001), pp. 751-762.
    by D Thirumalai, Woodson, DK Klimov
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Statistics of RNA melting kinetics
    Eur.\ Biophys.\ J., Vol. 23 (1994), pp. 29-38.
    by M Tacker, W Fontana, PF Stadler, P Schuster
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Recursive approaches to the statistical physics of lattice protein
    (1994)
    by P Stolorz
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Towards a Theory of Landscapes.
    (1996), pp. 77-163.
    by PF Stadler
    edited by Lopéz, R Capovilla, García R Pelayo, H Waelbroeck, F Zertuche
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • A path planning-based study of protein folding with a case study of hairpin formation in protein G and L
    (2003), pp. 240-251.
    by G Song, S Thomas, KA Dill, M Scholtz, NM Amato
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Monte Carlo Methods for the Self-Avoiding Walk
    (1996)
    by AD Sokal
    edited by Kurt Binder
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Folding kinetics of proteinlike heteropolymers
    J.\ Chem.\ Phys., Vol. 101 (1994), pp. 1519-1528.
    by ND Socci, JN Onuchic
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Simulations of the Folding of a Globular Protein
    Science, Vol. 250 (1990), pp. 1121-1125.
    by J Skolnick, A Kolinski
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • All-Atom Structure Prediction and Folding Simulations of a Stable Protein
    JACS, Vol. 124 (2002), pp. 11258-11259.
    by C Simmerling, B Strockbine, AE Roitberg
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Exploring the space of protein folding Hamiltonian: The balance of forces in a minimalist $β$-barrel model
    J.\ Chem.\ Phys., Vol. 109 (1998), pp. 2895-2903.
    by JE Shea, YD Nochomovitz, Z Guo, Brooks CL iii
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • From Folding Theories to Folding Proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding
    Annu.\ Rev.\ Phys.\ Chem., Vol. 52 (2001), pp. 499-535.
    by JE Shea, Brooks CL iii
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    Science, Vol. 289 (2000), pp. 448-452.
    by EA Schultes, DP Bartes
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • The factors affecting the stability of hydrogen-binded polypeptide structures in solution
    J.\ Chem.\ Phys., Vol. 62 (1958)
    by JA Schellman
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • A designed four helix bundle protein with native-like structure
    Nature\ Struct.\ Biol., Vol. 4 (1997), pp. 1039-1046.
    by CE Schafmeister, SL Laporte, LJW Miercke, RM Stroud
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Kinetics of Protein Folding
    J.\ Mol.\ Biol., Vol. 235 (1994), pp. 1614-1636.
    by A \usali, E Shakhnovich, M Karplus
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • How does a protein fold?
    Nature, Vol. 369 (1994), pp. 248-251.
    by A \usali, E Shakhnovich, M Karplus
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Principles of Nucleic-Acid Structure
    (1984)
    by W Saenger
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    Bioinformatics, Vol. 20 (2004), pp. 58-66.
    by J Ruan, GD Stormo, W Zhang
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • A dynamic programming algorithm for RNA structure prediction incuding pseudoknots
    J.\ Mol.\ Biol., Vol. 285 (1999), pp. 2053-2068.
    by E Rivas, SR Eddy
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Exploring the Fitness Landscapes of Lattice Proteins
    (1997)
    by A Renner, Bornberg E Bauer
    edited by RB Altman, K Dunker, L Hunter, TE Klein
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Self-Avoiding Walk Models for Non-Random Heteropolymers
    (1996)
    by A Renner, Bornberg E Bauer, IL Hofacker, PK Schuster, PF Stadler
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Self avoiding walks and lattice proteins
    (1994)
    by A Renner
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Combinatorial Landscapes
    SIAM Review, Vol. 44 (2002), pp. 3-54.
    by CM Reidys, PF Stadler
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Improved efficiency of RNA secondary structure prediction in cluding pseudoknots
    (2002)
    by J Reeder, R Giegerich
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • On three-dimensional self-avoiding walks
    J.\ Phys.\ A:\ Math.\ Gen., Vol. 18 (1985), pp. 113-126.
    by DC Rapaport
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
  • Co-ordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis: Control by transcriptional antitermination involving a conserved regulatory sequence.
    EMBO J., Vol. 11 (1992), pp. 3117-3127.
    by H Putzer, N Gendron, Grunberg M Manago
    posted to bibtex-import by mtw on 2006-09-05 20:11:43 as **
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