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Group: SGU-CIPF - with tag biophysics [90 articles]

Недавние статьи, отправленные по почте членами SGU-CIPF группы with tag biophysics
  • RNA conformational classes.
    Nucleic Acids Res, Vol. 32, No. 5. (2004), pp. 1666-1677.
    by B Schneider, Z Morávek, HM Berman
    posted to rotamers rna classification biophysics by marcius to the group SGU-CIPF on 2007-06-12 12:55:21 as ** along with 1 person and 1 group emidio_capriotti BioinfoCIPF
  • The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
    Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119.
    by JS McCaskill
    posted to algorithms biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-10-20 14:24:37 as ** along with 5 people and 2 groups evaf arcticrasta condon Hosna Kiarostami beta BioinfoCIPF
  • Recent advances in the development and application of implicit solvent models in biomolecule simulations.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 217-224.
    by M Feig, CL Brooks
    posted to biophysics foce_field folding protein_structure review by marcius to the group SGU-CIPF on 2006-10-02 10:50:01 as ** along with 5 people and 1 group apostola simone ttjoseph gane5h RamuAnandakrishnan BioinfoCIPF
  • Effective energy functions for protein structure prediction.
    Curr Opin Struct Biol, Vol. 10, No. 2. (April 2000), pp. 139-145.
    by T Lazaridis, M Karplus
    posted to biophysics foce_field folding protein_structure review by marcius to the group SGU-CIPF on 2006-10-02 10:49:24 as ** along with 2 people and 1 group karbak nigham BioinfoCIPF
  • Empirical force fields for biological macromolecules: Overview and issues
    Journal of Computational Chemistry, Vol. 25, No. 13. (1 July 2004), pp. 1584-1604.
    by Alexander D Mackerell
    posted to biophysics foce_field folding protein_structure review by marcius to the group SGU-CIPF on 2006-10-02 10:47:07 as ** along with 5 people and 1 group BragilMassoud dgront loison mirzazadeh AndreaColetta BioinfoCIPF
  • Force fields for protein simulations.
    Adv Protein Chem, Vol. 66 (2003), pp. 27-85.
    by JW Ponder, DA Case
    posted to biophysics foce_field folding protein_structure review by marcius to the group SGU-CIPF on 2006-10-02 10:46:40 as ** along with 3 people and 1 group karbak papatonyhill hmk BioinfoCIPF
  • Thermodynamics of protein folding: a microscopic view.
    Biophys Chem, Vol. 100, No. 1-3. (2003), pp. 367-395.
    by T Lazaridis, M Karplus
    posted to biophysics foce_field folding protein_structure review by marcius to the group SGU-CIPF on 2006-10-02 10:46:31 as ** along with 1 person and 1 group karbak BioinfoCIPF
  • Sampling Realistic Protein Conformations Using Local Structural Bias
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e131.
    by Thomas Hamelryck, John T Kent, Anders Krogh
    posted to biophysics clustering computational_biology dynamics structure by marcius to the group SGU-CIPF on 2006-09-29 08:57:03 as ** along with 1 person and 1 group mijam BioinfoCIPF
  • Evolution of alternative transcriptional circuits with identical logic
    Nature, Vol. 443, No. 7110. (2006), pp. 415-420.
    by Annie E Tsong, Brian B Tuch, Hao Li, Alexander D Johnson
    posted to bioengineering bioinformatics biophysics by marcius to the group SGU-CIPF on 2006-09-28 09:03:32 as ** along with 6 people and 3 groups brant adepace aswin srfairclough cisevol emptyhb EisenLab BioinfoCIPF cis-regulatory-evolution
  • How do RNA folding algorithms work?
    Nature Biotechnology, Vol. 22, No. 11., 1457.
    by Sean R Eddy
    posted to algorithms bioinformatics biophysics folding review rna by marcius to the group SGU-CIPF on 2006-09-08 11:14:16 as ** along with 10 people and 1 group evaf tardigrade mtagaya 3times3 cthachuk magnolia maralena guxiyou cambray austin BioinfoCIPF
  • Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450.
    by ME Hatley, SW Lockless, SK Gibson, AG Gilman, R Ranganathan
    posted to allosteric bioinformatics biophysics statistical_potentials by marcius to the group SGU-CIPF on 2006-08-09 16:38:51 as ** along with 4 people and 4 groups barry lna Einat caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF
  • Structural determinants of allosteric ligand activation in RXR heterodimers.
    Cell, Vol. 116, No. 3. (6 February 2004), pp. 417-429.
    by AI Shulman, C Larson, DJ Mangelsdorf, R Ranganathan
    posted to allosteric bioinformatics biophysics statistical_potentials by marcius to the group SGU-CIPF on 2006-08-09 16:38:37 as ** along with 3 people and 2 groups lna gbart caporaso biomedical-nlp BioinfoCIPF
  • Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.
    Nucleic Acids Res, Vol. 31, No. 24. (15 December 2003), pp. 7131-7140.
    by Y Pan, AD MacKerell
    posted to biophysics dna molecular_dynamics rna structure by marcius to the group SGU-CIPF on 2006-07-28 12:39:42 as ** along with 1 person and 1 group Elena_Zubova BioinfoCIPF
  • From sequences to shapes and back: a case study in RNA secondary structures.
    Proc R Soc Lond B Biol Sci, Vol. 255, No. 1344. (22 March 1994), pp. 279-284.
    by P Schuster, W Fontana, PF Stadler, IL Hofacker
    posted to bioinformatics biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-07-28 12:38:26 as ** along with 3 people and 1 group evaf ilh mtw BioinfoCIPF
  • The correlation between protein stability and dipole moment: a critical test
    Protein Engineering, Design and Selection, Vol. 19, No. 8. (August 2006), pp. 355-358.
    by Wunderlich, Michael, Schmid, X Franz
    posted to biophysics experimental protein stability structure by marcius to the group SGU-CIPF on 2006-07-26 14:35:56 as ** along with 1 group BioinfoCIPF
  • Efficient computation of RNA folding dynamics
    Journal of Physics A: Mathematical and General, Vol. 37, No. 17. (2004), pp. 4731-4741.
    by Michael T Wolfinger, Andreas, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-07-24 17:47:12 as ** along with 2 people and 1 group ilh mtw BioinfoCIPF
  • Mass spectrometry of RNA
    Trends in Biochemical Sciences, Vol. 31, No. 3. (March 2006), pp. 173-181.
    by Benjamin Thomas, Alexandre V Akoulitchev
    posted to biophysics rna structure by marcius to the group SGU-CIPF on 2006-07-20 12:23:20 as ** along with 1 person and 2 groups cdawson BioinfoCIPF GIG
  • Structural biologyProteins downhill all the way
    Nature, Vol. 442, No. 7100. (19 July 2006), pp. 255-256.
    by Jeffery W Kelly
    posted to biophysics folding news protein_structure views by marcius to the group SGU-CIPF on 2006-07-20 10:06:15 as ** along with 1 group BioinfoCIPF
  • Atom-by-atom analysis of global downhill protein folding
    Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321.
    by Mourad Sadqi, David Fushman, Victor Muñoz
    posted to biophysics folding protein_structure by marcius to the group SGU-CIPF on 2006-07-20 10:05:38 as ** along with 4 people and 1 group wouterboomsma choonpeng gisle huyun110 BioinfoCIPF
  • Emergence of protein fold families through rational design.
    PLoS Comput Biol, Vol. 2, No. 7. (7 July 2006)
    by F Ding, NV Dokholyan, E Shakhnovich
    posted to biophysics classification protein_domains by marcius to the group SGU-CIPF on 2006-07-19 10:40:04 as ** along with 2 people and 1 group insectopalo kgutwin BioinfoCIPF
  • Co-transcriptional folding is encoded within RNA genes.
    BMC Mol Biol, Vol. 5, No. 1. (6 August 2004)
    by IM Meyer, I Miklós
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-07-18 12:23:54 as ** along with 4 people and 2 groups evaf condon Hosna raylim beta BioinfoCIPF
  • Design of multistable RNA molecules.
    RNA, Vol. 7, No. 2. (February 2001), pp. 254-265.
    by C Flamm, IL Hofacker, S Maurer-Stroh, PF Stadler, M Zehl
    posted to bioengineering biophysics rna by marcius to the group SGU-CIPF on 2006-07-18 10:33:37 as ** along with 3 people and 1 group evaf ilh mtw BioinfoCIPF
  • Strategies for RNA folding and assembly.
    Nat Rev Mol Cell Biol, Vol. 5, No. 11. (November 2004), pp. 908-919.
    by R Schroeder, A Barta, K Semrad
    posted to biophysics folding review rna by marcius to the group SGU-CIPF on 2006-07-13 10:25:25 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • Predicting RNA secondary structure by free energy minimization
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) (May 2006), pp. 1-9.
    by David Mathews
    posted to biophysics review rna secondary_structure by marcius to the group SGU-CIPF on 2006-05-19 22:16:43 as ** along with 5 people and 2 groups condon Hosna hesam cthachuk apop beta BioinfoCIPF
  • Fast evaluation of internal loops in RNA secondary structure prediction
    Bioinformatics, Vol. 15, No. 6. (1 June 1999), pp. 440-445.
    by Rb Lyngso, M Zuker, Cn Pedersen
    posted to biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-05-19 18:29:34 as ** along with 2 people and 2 groups arcticrasta condon beta BioinfoCIPF
  • Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
    BMC Bioinformatics, Vol. 5 (4 August 2004)
    by J Reeder, R Giegerich
    posted to biophysics folding rna secondary_structure by marcius to the group SGU-CIPF on 2006-05-18 09:02:38 as ** along with 4 people and 2 groups eckart_bindewald arcticrasta condon Hosna beta BioinfoCIPF
  • Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
    BMC Bioinformatics, Vol. 7, No. 1. (27 March 2006)
    by Andrew V Uzilov, Joshua M Keegan, David H Mathews
    posted to biophysics ncrna secondary_structure by marcius to the group SGU-CIPF on 2006-05-18 00:17:28 as ** along with 2 people and 1 group alexg eckart_bindewald BioinfoCIPF
  • Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States
    Journal of Molecular Biology, Vol. 359, No. 2. (2 June 2006), pp. 446-454.
    by Eda Koculi, D Thirumalai, Sarah A Woodson
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-05-17 00:38:30 as ** along with 1 group BioinfoCIPF
  • Energetics and cooperativity of tertiary hydrogen bonds in RNA structure.
    Biochemistry, Vol. 38, No. 27. (6 July 1999), pp. 8691-8702.
    by SK Silverman, TR Cech
    posted to biophysics rna structure by marcius to the group SGU-CIPF on 2006-05-15 22:55:04 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • RNA secondary structure: physical and computational aspects.
    Q Rev Biophys, Vol. 33, No. 3. (August 2000), pp. 199-253.
    by PG Higgs
    posted to bioinformatics biophysics review rna secondary_structure by marcius to the group SGU-CIPF on 2006-05-15 22:40:41 as ** along with 2 people and 1 group arcticrasta penka BioinfoCIPF
  • A complex adaptive systems approach to the kinetic folding of RNA.
    Biosystems, Vol. 82, No. 3. (December 2005), pp. 257-265.
    by W Ndifon
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-05-11 07:36:14 as ** along with 1 person and 1 group arcticrasta BioinfoCIPF
  • Thermodynamics of RNARNA binding
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1177-1182.
    by Ulrike Muckstein, Hakim Tafer, Jorg Hackermuller, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
    posted to biophysics docking rna by marcius to the group SGU-CIPF on 2006-05-09 03:57:48 as ** along with 1 person and 1 group Hosna BioinfoCIPF
  • RNALOSS: a web server for RNA locally optimal secondary structures.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by P Clote
    posted to bioinformatics biophysics databases secondary_structure servers by marcius to the group SGU-CIPF on 2006-05-05 23:27:04 as ** along with 2 people and 2 groups arcticrasta condon beta BioinfoCIPF
  • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230.
    by Arthur M Lesk, Cyrus Chothia
    posted to biophysics comparative_modeling evolution protein_structure by marcius to the group SGU-CIPF on 2006-04-30 01:12:36 as ** along with 2 people and 3 groups ana barry structural_bioinformatics Bioinformatics BioinfoCIPF
  • Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, Vol. 49, No. 2. (February 1999), pp. 145-165.
    by S Wuchty, W Fontana, IL Hofacker, P Schuster
    posted to biophysics folding rna secondary_structure by marcius to the group SGU-CIPF on 2006-04-30 01:11:30 as ** along with 3 people and 1 group eckart_bindewald arcticrasta ilh BioinfoCIPF
  • Beyond kinetic traps in RNA folding
    Current Opinion in Structural Biology, Vol. 11, No. 3. (1 June 2001), pp. 309-314.
    by Daniel K Treiber, James R Williamson
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-04-30 01:10:59 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • Physical Origins of Protein Superfamilies.
    J Mol Biol (6 February 2006)
    by Konstantin B B Zeldovich, Igor N N Berezovsky, Eugene I I Shakhnovich
    posted to biophysics computational_biology evolution protein structure by marcius to the group SGU-CIPF on 2006-04-27 20:29:04 as ** along with 3 people and 2 groups Einat laurabailey happy_manatee structural_bioinformatics BioinfoCIPF
  • Stitching together RNA tertiary architectures
    Journal of Molecular Biology, Vol. 294, No. 4. (10 December 1999), pp. 829-849.
    by Thomas Hermann, Dinshaw J Patel
    posted to biophysics folding rna structure by marcius to the group SGU-CIPF on 2006-04-24 07:42:53 as ** along with 3 people and 2 groups ttjoseph condon jarasch beta BioinfoCIPF
  • Predicting free energy landscapes for complexes of double-stranded chain molecules
    The Journal of Chemical Physics, Vol. 114, No. 9. (2001), pp. 4253-4266.
    by Wenbing Zhang, Shi J Chen
    posted to biophysics computational_biology dna folding rna by marcius to the group SGU-CIPF on 2006-04-21 22:11:14 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • Theory for the conformational changes of double-stranded chain molecules
    The Journal of Chemical Physics, Vol. 109, No. 11. (1998), pp. 4602-4616.
    by Shi J Chen, Ken A Dill
    posted to biophysics computational_biology dna folding rna by marcius to the group SGU-CIPF on 2006-04-21 22:11:01 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • Statistical thermodynamics of double-stranded polymer molecules
    The Journal of Chemical Physics, Vol. 103, No. 13. (1995), pp. 5802-5813.
    by Shi J Chen, Ken A Dill
    posted to biophysics computational_biology dna folding rna by marcius to the group SGU-CIPF on 2006-04-21 22:10:14 as ** along with 1 person and 2 groups condon beta BioinfoCIPF
  • RNA folding energy landscapes
    PNAS, Vol. 97, No. 2. (18 January 2000), pp. 646-651.
    by Shi-Jie Chen, Ken A Dill
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-04-21 22:09:25 as ** along with 3 people and 2 groups condon mtw ARobson beta BioinfoCIPF
  • Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.
    Bioinformatics, Vol. 21, No. 17. (1 September 2005), pp. 3516-3523.
    by J Reeder, R Giegerich
    posted to bioinformatics biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-04-19 10:55:07 as ** along with 2 people and 2 groups andersbj arcticrasta microRNA BioinfoCIPF
  • A comparison of RNA folding measures.
    BMC Bioinformatics, Vol. 6, No. 1. (3 October 2005)
    by Eva Freyhult, Paul P Gardner, Vincent Moulton
    posted to biophysics folding rna by marcius to the group SGU-CIPF on 2006-04-18 19:11:54 as ** along with 5 people and 3 groups imouthesmp eckart_bindewald mtagaya bsmagic Kiarostami Bioinformatics BioinfoCIPF bioinplant
  • Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
    Bioinformatics, Vol. 22, No. 8. (15 April 2006), pp. 1007-1009.
    by Surjit B Dixit, David L Beveridge
    posted to bioinformatics biophysics dna molecular_dynamics by marcius to the group SGU-CIPF on 2006-04-17 04:35:18 as ** along with 1 group BioinfoCIPF
  • Derivation of rules for comparative protein modeling from a database of protein structure alignments.
    Protein Sci, Vol. 3, No. 9. (September 1994), pp. 1582-1596.
    by A Sali, JP Overington
    posted to bioinformatics biophysics comparative_modeling structure_prediction by marcius to the group SGU-CIPF on 2006-04-08 07:26:12 as ** along with 2 people and 3 groups ana bicko structural_bioinformatics Bioinformatics BioinfoCIPF
  • Comparison of P-RnaPredict and mfoldalgorithms for RNA secondary structure prediction
    Bioinformatics, Vol. 22, No. 8. (15 April 2006), pp. 934-942.
    by Kay C Wiese, Andrew Hendriks
    posted to bioinformatics biophysics rna secondary_structure by marcius to the group SGU-CIPF on 2006-04-08 00:08:21 as ** along with 1 group BioinfoCIPF
  • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
    Nucleic Acids Res, Vol. 9, No. 1. (10 January 1981), pp. 133-148.
    by M Zuker, P Stiegler
    posted to ab-initio biophysics folding rna by marcius to the group SGU-CIPF on 2006-03-18 20:59:28 as ** along with 5 people and 1 group evaf arcticrasta mtagaya Hosna guxiyou BioinfoCIPF
  • Evidence that miRNAs are different from other RNAs.
    Cell Mol Life Sci, Vol. 63, No. 2. (January 2006), pp. 246-254.
    by BH Zhang, XP Pan, SB Cox, GP Cobb, TA Anderson
    posted to biophysics computational_biology microrna by marcius to the group SGU-CIPF on 2006-03-17 18:48:36 as ** along with 4 people and 5 groups eckart_bindewald andersbj dchughes cdawson microRNA G4ID BioinfoCIPF GIG Genetics-of-Gambling
  • Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
    J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196.
    by LA Mirny, EI Shakhnovich
    posted to biophysics evolution folding by marcius to the group SGU-CIPF on 2006-03-14 17:21:55 as ** along with 3 people and 3 groups ana barry Einat structural_bioinformatics Bioinformatics BioinfoCIPF
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