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j3xucites library [381 articles]

Neue Artikel in j3xucites Bibliothek.
  • Benchmarking template selection and model quality assessment
    by David Jones
    posted to threading by j3xucite on 2008-05-20 03:39:44 as **
  • A composite score for predicting errors in protein structure models.
    Protein Sci, Vol. 15, No. 7. (July 2006), pp. 1653-1666.
    by D Eramian, MY Shen, D Devos, F Melo, A Sali, MA Marti-Renom
    posted to model assessment by j3xucite on 2008-05-07 23:30:47 as ** along with 4 people dimka vavi wouterboomsma mijam
  • Wiley InterScience :: Article :: HTML Full Text
    posted to reconstruction backbone by j3xucite on 2008-04-29 03:52:16 as **
  • Novel knowledge-based mean force potential at the profile level
    BMC Bioinformatics, Vol. 7 (27 June 2006), 324.
    by Qiwen Dong, Xiaolong Wang, Lei Lin
    posted to energy function by j3xucite on 2008-03-24 04:38:34 as ** along with 1 person aengisch
  • OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing
    Journal of Molecular Biology, Vol. 376, No. 1. (8 February 2008), pp. 288-301.
    by Mingyang Lu, Athanasios D Dousis, Jianpeng Ma
    posted to energy function by j3xucite on 2008-03-24 04:37:40 as ** along with 1 person cdeane
  • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Sitao Wu, Yang Zhang
    posted to protein threading by j3xucite on 2008-03-19 21:13:34 as ** along with 1 person chad_davis
  • Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas Huber
    posted to cis-proline by j3xucite on 2008-02-28 22:07:31 as **
  • Local protein structure prediction using discriminative models.
    BMC Bioinformatics, Vol. 7, No. 1. (11 January 2006)
    by Oliver Sander, Ingolf Sommer, Thomas Lengauer
    posted to local prediction structure by j3xucite on 2008-02-24 04:42:43 as ** along with 1 person chad_davis
  • Protein folding by a biased Monte Carlo procedure in the dihedral angle space.
    FASEB J, Vol. 10, No. 1. (January 1996), pp. 119-125.
    by B Lee, N Kurochkina, HS Kang
    posted to folding protein by j3xucite on 2008-02-23 03:31:25 as **
  • The COG database: an updated version includes eukaryotes.
    BMC Bioinformatics, Vol. 4 (11 September 2003)
    by RL Tatusov, ND Fedorova, JD Jackson, AR Jacobs, B Kiryutin, EV Koonin, DM Krylov, R Mazumder, SL Mekhedov, AN Nikolskaya, BS Rao, S Smirnov, AV Sverdlov, S Vasudevan, YI Wolf, JJ Yin, DA Natale
    posted to cog by j3xucite on 2008-02-22 22:19:36 as ** along with 6 people and 1 group natstreet arve indigoviolet treangen bluto westoll EisenLab
  • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
    Science, Vol. 282, No. 5389. (23 October 1998), pp. 740-744.
    by Y Duan, PA Kollman
    posted to dynamics molecular by j3xucite on 2008-02-19 16:22:17 as ** along with 3 people choonpeng RamuAnandakrishnan allmensch
  • A backbone-based theory of protein folding.
    Proc Natl Acad Sci U S A (30 October 2006)
    by George D D Rose, Patrick J J Fleming, Jayanth R R Banavar, Amos Maritan
    posted to folding protein by j3xucite on 2008-02-18 19:29:45 as ** along with 3 people marck thaliana choonpeng
  • A knowledge-based move set for protein folding
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 682-688.
    by William W Chen, Jae S Yang, Eugene I Shakhnovich
    posted to sampling by j3xucite on 2008-02-15 20:46:46 as **
  • Computational techniques for efficient conformational sampling of proteins
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, Harold A Scheraga
    posted to conformational sampling by j3xucite on 2008-02-15 20:35:58 as **
  • Dynamic Conditional Random Fields: Factorized Probabilistic Models for Labeling and Segmenting Sequence Data
    J. Mach. Learn. Res., Vol. 8 (2007), pp. 693-723.
    by Charles Sutton, Andrew Mccallum, Khashayar Rohanimanesh
    posted to crf by j3xucite on 2008-02-14 21:29:42 as ** along with 1 person and 1 group bundschu generif_paper
  • The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions
    Protein Sci (22 January 2007), ps.062447107.
    by Velin Z Spassov, Lisa Yan, Paul K Flook
    posted to chain protein side by j3xucite on 2008-02-01 16:55:04 as **
  • Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.
    Proteins (17 September 2007)
    by Riccardo M M Bennett-Lovsey, Alex D D Herbert, Michael J E J Sternberg, Lawrence A A Kelley
    posted to fold recognition by j3xucite on 2008-01-31 16:59:12 as ** along with 1 person cdeane
  • Propensities, probabilities, and the Boltzmann hypothesis
    Protein Sci, Vol. 12, No. 6. (1 June 2003), pp. 1298-1302.
    by David Shortle
    posted to folding protein by j3xucite on 2008-01-25 05:28:14 as **
  • Probabilistic sampling of protein conformations: New hope for brute force?
    Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (2002), pp. 8-23.
    by Howard J Feldman, Christopher WV Hogue
    posted to conformation protein sampling by j3xucite on 2008-01-24 20:40:39 as **
  • P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins
    Comput. Appl. Biosci., Vol. 13, No. 3. (1 June 1997), pp. 291-295.
    by G Labesse, N Colloc'h, J Pothier, JP Mornon
    posted to protein structure by j3xucite on 2008-01-15 22:19:38 as ** along with 2 people thamelry wouterboomsma
  • A simplified representation of protein conformations for rapid simulation of protein folding
    Journal of Molecular Biology, Vol. 104 (1976), pp. 59-107.
    by M Levitt
    posted to folding protein by j3xucite on 2008-01-14 02:21:59 as **
  • SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    J Mol Biol, Vol. 247, No. 4. (7 April 1995), pp. 536-540.
    by AG Murzin, SE Brenner, T Hubbard, C Chothia
    posted to protein structure by j3xucite on 2008-01-13 04:26:09 as ** along with 9 people sim82 dimka chrn chad_davis sriram_s aengisch massivemayhem cjeans siebertm
  • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    Journal of Molecular Biology, Vol. 266, No. 4. (7 March 1997), pp. 831-846.
    by Britt H Park, Enoch S Huang, Michael Levitt
    posted to energy function by j3xucite on 2008-01-13 04:15:37 as ** along with 2 people wilbur Alois
  • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    Journal of Molecular Biology, Vol. 275, No. 5. (6 February 1998), pp. 895-916.
    by Ram Samudrala, John Moult
    posted to energy function by j3xucite on 2008-01-13 04:13:02 as **
  • Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm.
    Proteins, Vol. 56, No. 3. (15 August 2004), pp. 502-518.
    by J Skolnick, D Kihara, Y Zhang
    posted to threading by j3xucite on 2008-01-12 19:59:20 as ** along with 1 person schuylrp
  • TM-align: a protein structure alignment algorithm based on the TM-score.
    Nucleic Acids Res, Vol. 33, No. 7. (2005), pp. 2302-2309.
    by Y Zhang, J Skolnick
    posted to alignment structure by j3xucite on 2008-01-12 19:58:11 as ** along with 1 person aengisch
  • Ab initio construction of protein tertiary structures using a hierarchical approach.
    J Mol Biol, Vol. 300, No. 1. (30 June 2000), pp. 171-185.
    by Y Xia, ES Huang, M Levitt, R Samudrala
    posted to folding protein by j3xucite on 2008-01-11 02:45:22 as ** along with 1 person aengisch
  • A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics
    Journal of Molecular Biology, Vol. 329, No. 1. (23 May 2003), pp. 159-174.
    by Chen Keasar, Michael Levitt
    posted to folding protein by j3xucite on 2007-12-21 18:06:39 as **
  • Reduced Cbeta statistical potentials can outperform all-atom potentials in decoy identification
    Protein Sci, Vol. 16, No. 10. (1 October 2007), pp. 2123-2139.
    by James E Fitzgerald, Abhishek K Jha, Andres Colubri, Tobin R Sosnick, Karl F Freed
    posted to energy by j3xucite on 2007-12-05 01:56:01 as **
  • Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
    posted to loop by j3xucite on 2007-11-21 06:53:57 as **
  • Stochastic Pairwise Alignments and Scoring Methods for Comparative Protein Structure Modeling
    posted to alignment protein by j3xucite on 2007-11-19 03:19:18 as **
  • Stochastic Pairwise Alignments and Scoring Methods for Comparative Protein Structure Modeling
    J. Chem. Inf. Model. (29 March 2007)
    by AC Marko, K Stafford, T Wymore
    posted to alignment protein by j3xucite on 2007-11-19 02:45:36 as ** along with 1 person daevans
  • In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling.
    J Mol Biol, Vol. 328, No. 3. (2 May 2003), pp. 593-608.
    by B Contreras-Moreira, PW Fitzjohn, PA Bates
    posted to protein threading by j3xucite on 2007-11-18 01:17:01 as ** along with 1 person ujh
  • In search for more accurate alignments in the twilight zone
    Protein Sci, Vol. 11, No. 7. (1 July 2002), pp. 1702-1713.
    by Lukasz Jaroszewski, Weizhong Li, Adam Godzik
    posted to protein by j3xucite on 2007-11-15 23:00:30 as **
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. e112-e112.
    by Chivian, Dylan, Baker, David
    posted to protein by j3xucite on 2007-11-15 17:18:46 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Distributions in Protein Conformation Space: Implications for Structure Prediction and Entropy
    Biophysical Journal (2004)
    posted to protein by j3xucite on 2007-11-10 05:07:42 as **
  • A fast method to sample real protein conformational space
    Proteins: Structure, Function, and Genetics, Vol. 39, No. 2. (2000), pp. 112-131.
    by Howard J Feldman, Christopher WV Hogue
    posted to protein by j3xucite on 2007-11-10 04:43:18 as ** along with 1 person apaydin
  • Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.
    J Comput Chem, Vol. 28, No. 9. (15 July 2007), pp. 1593-1597.
    by D Gront, S Kmiecik, A Kolinski
    posted to protein by j3xucite on 2007-11-09 15:18:04 as ** along with 4 people wouterboomsma dgront sekmi mijam
  • A replica exchange Monte Carlo algorithm for protein folding in the HP model
    BMC Bioinformatics, Vol. 8 (17 September 2007), 342.
    by Chris Thachuk, Alena Shmygelska, Holger H Hoos
    posted to search by j3xucite on 2007-11-09 15:16:26 as ** along with 3 people iantunbridge insectopalo saunders
  • TOUCHSTONE II: a new approach to ab initio protein structure prediction.
    Biophys J, Vol. 85, No. 2. (August 2003), pp. 1145-1164.
    by Y Zhang, A Kolinski, J Skolnick
    posted to protein by j3xucite on 2007-11-08 16:18:05 as ** along with 1 person mkurc
  • TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
    Proceedings of the National Academy of Sciences, Vol. 98, No. 18. (28 August 2001), pp. 10125-10130.
    by Daisuke Kihara, Hui Lu, Andrzej Kolinski, Jeffrey Skolnick
    posted to protein by j3xucite on 2007-11-08 16:17:34 as **
  • From the Cover: The network of sequence flow between protein structures
    Proceedings of the National Academy of Sciences, Vol. 104, No. 28. (10 July 2007), pp. 11627-11632.
    by Leonid Meyerguz, Jon Kleinberg, Ron Elber
    posted to protein by j3xucite on 2007-11-07 16:41:03 as **
  • OPUS-Ca: A knowledge-based potential function requiring only Calpha positions
    Protein Sci, Vol. 16, No. 7. (1 July 2007), pp. 1449-1463.
    by Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li, Jianpeng Ma
    posted to energy function by j3xucite on 2007-11-06 03:28:00 as **
  • HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.
    J Mol Biol, Vol. 301, No. 1. (4 August 2000), pp. 173-190.
    by C Bystroff, V Thorsson, D Baker
    posted to protein structure by j3xucite on 2007-11-05 16:51:01 as ** along with 4 people and 1 group wenhan wouterboomsma dgront rabio MBLAB
  • The Fisher-Bingham Distribution on the Sphere
    Journal of Royal Statistical Society, Vol. 44 (1982), pp. 71-80.
    by John T Kent
    posted to fb by j3xucite on 2007-11-02 17:54:25 as **
  • Maximum Likelihood from Incomplete Data via the EM Algorithm
    Journal of the Royal Statistical Society, Vol. 39, No. 1. (1977), pp. 1-38.
    by AP Dempster, NM Laird, DB Rubin
    posted to em by j3xucite on 2007-11-02 17:50:40 as ** along with 43 people and 8 groups iansimon qwermish wenhan eegilbert weymouth jake ingo anoopsarkar gangli rpadams wkw hoangmtbk dragonrez Freyr lukec dheena songhaoyuan amirsaemi ecome walkking nandan marrtin tvdbulck MichaelDonoser MikeDoni rwilliamson calamar qq987 ichbins81 petrposik ggorjan shiquanwang lcigler ciga kvorg ifejobi DavidSchulz ykuoka singhsh trop_wizz eddymier schulz stkhu MBLAB Statistics_and_Social_Science tulip LTN Computer_Graphics Computational_Information_Geometry csb_journal_club_public Medical Image Analysis and Visualization @ OSU
  • Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.
    Journal Molecular Biology, Vol. 218, No. 1. (5 March 1991), pp. 183-194.
    by L Holm, C Sander
    posted to protein structure by j3xucite on 2007-11-02 17:45:28 as ** along with 3 people and 2 groups jwm wouterboomsma dgront Radiation_Damage Stressosome
  • PISCES: a protein sequence culling server.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1589-1591.
    by G Wang, RL Dunbrack
    posted to protein structure by j3xucite on 2007-11-02 17:43:43 as ** along with 8 people and 2 groups barry aalibes kaarsinogen dgront blackbart mloewer ezralanglois chgjb structural_bioinformatics Bioinformatics
  • SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.
    Nucleic Acids Research, Vol. 34, No. Web Server issue. (1 July 2006)
    by J Maupetit, R Gautier, P Tufféry
    posted to protein structure by j3xucite on 2007-11-02 17:41:16 as **
  • Small libraries of protein fragments model native protein structures accurately.
    Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 297-307.
    by R Kolodny, P Koehl, L Guibas, M Levitt
    posted to protein structure by j3xucite on 2007-11-02 17:37:44 as ** along with 3 people and 2 groups ana barry eckart_bindewald structural_bioinformatics Bioinformatics
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