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Tag protein-structure [140 articles]

Recent papers classified by the tag protein-structure.
  • Sequence comparison and protein structure prediction.
    Curr Opin Struct Biol, Vol. 16, No. 3. (June 2006), pp. 374-384.
    by RL Dunbrack
    posted to protein-structure review by xiaobeizhao on 2006-10-09 04:00:40 as ** along with 5 people agustinarce wouterboomsma rabio schuylrp jwm
  • Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight.
    J Mol Model (Online) (7 October 2006)
    by Rajani R Joshi, Vivekanand V Samant
    posted to domain-finding protein-structure by wouterboomsma on 2006-10-16 17:54:35 as **
  • Progress in structure prediction of alpha-helical membrane proteins.
    Curr Opin Struct Biol (3 July 2006)
    by Sarel J J Fleishman, Nir Ben-Tal
    posted to protein-structure review by wouterboomsma on 2006-07-24 14:26:30 as ** along with 1 person and 1 group xdeupi LabCompMed
  • 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 Muã±oz
    posted to protein-structure by wouterboomsma on 2006-07-31 17:25:53 as ** along with 4 people and 2 groups marcius choonpeng gisle huyun110 BioinfoCIPF SGU-CIPF
  • Potential for assessing quality of protein structure based on contact number prediction.
    Proteins (20 June 2006)
    by Takashi Ishida, Shugo Nakamura, Kentaro Shimizu
    posted to protein-structure quality-assessment by wouterboomsma on 2006-07-24 13:53:32 as **
  • All-atom ab initio folding of a diverse set of proteins.
    Structure, Vol. 15, No. 1. (January 2007), pp. 53-63.
    by JS Yang, WW Chen, J Skolnick, EI Shakhnovich
    posted to protein-structure energy-function by wouterboomsma on 2007-02-05 11:42:46 as *** along with 1 person choonpeng
  • Statistical potential for assessment and prediction of protein structures.
    Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2507-2524.
    by MY Shen, A Sali
    posted to energy-function protein-structure by wouterboomsma on 2006-11-09 16:12:15 as ** along with 4 people kgutwin j3xucite cdeane dimka
  • Funnel sculpting for in silico assembly of secondary structure elements of proteins
    PNAS, Vol. 100, No. 19. (16 September 2003), pp. 10700-10705.
    by Boris Fain, Michael Levitt
    posted to energy-function protein-structure by wouterboomsma on 2006-04-10 10:03:11 as **
  • The protein folding problem: when will it be solved?
    Curr Opin Struct Biol (13 June 2007)
    by Ken A A Dill, S Banu B Ozkan, Thomas R R Weikl, John D D Chodera, Vincent A A Voelz
    posted to protein-structure review by wouterboomsma on 2007-07-09 10:49:08 as read along with 6 people cat_worth cactus Jporci cdeane kalicuta sebk
  • Novel approach for alpha-helical topology prediction in globular proteins: Generation of interhelical restraints.
    Proteins (6 October 2006)
    by S R R McAllister, B E E Mickus, J L L Klepeis, C A A Floudas
    posted to local-structure protein-structure by wouterboomsma on 2006-10-16 17:53:25 as **
  • Replica-exchange Monte Carlo scheme for bayesian data analysis.
    Phys Rev Lett, Vol. 94, No. 1. (14 January 2005)
    by M Habeck, M Nilges, W Rieping
    posted to mcmc protein-structure by wouterboomsma on 2006-04-11 11:30:51 as read along with 3 people apaydin dimka dgront
  • Some fundamental aspects of building protein structures from fragment libraries.
    Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650.
    by JB Holmes, J Tsai
    posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:57:29 as read along with 2 people and 2 groups barry eckart_bindewald structural_bioinformatics Bioinformatics
  • 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.
    J Mol Biol, Vol. 218, No. 1. (5 March 1991), pp. 183-194.
    by L Holm, C Sander
    posted to protein-structure representation by wouterboomsma on 2006-04-11 11:04:13 as read along with 3 people and 2 groups jwm j3xucite dgront Radiation_Damage Stressosome
  • Protein folding: from the levinthal paradox to structure prediction.
    J Mol Biol, Vol. 293, No. 2. (22 October 1999), pp. 283-293.
    by B Honig
    posted to energy-function protein-structure review by wouterboomsma on 2006-04-18 13:38:26 as read
  • Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.
    BMC Bioinformatics, Vol. 6 (28 June 2005)
    by W Boomsma, T Hamelryck
    posted to loop-closure protein-structure by wouterboomsma on 2006-04-10 10:31:14 as read along with 3 people pansapiens vavi Alan
  • Characterization of protein-folding pathways by reduced-space modeling.
    Proc Natl Acad Sci U S A, Vol. 104, No. 30. (24 July 2007), pp. 12330-12335.
    by S Kmiecik, A Kolinski
    posted to folding-pathways protein-structure by wouterboomsma on 2007-07-30 09:20:45 as ** along with 3 people mkurc sekmi nh
  • Folding proteins with a simple energy function and extensive conformational searching.
    Protein Sci, Vol. 5, No. 2. (February 1996), pp. 254-261.
    by K Yue, KA Dill
    posted to protein-structure by wouterboomsma on 2007-02-26 12:35:49 as read
  • Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors.
    Proteins (13 February 2006)
    by Jinfeng Zhang, Rong Chen, Jie Liang
    posted to energy-function protein-structure by wouterboomsma on 2006-04-10 10:20:07 as ** along with 1 person cdeane
  • HARMONY: a server for the assessment of protein structures.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by G Pugalenthi, K Shameer, N Srinivasan, R Sowdhamini
    posted to protein-structure quality-assessment servers by wouterboomsma on 2006-07-24 14:39:00 as ** along with 3 people bicko skhadar wilbur
  • Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction.
    Proteins (25 August 2006)
    by Bin-Guang G Ma, Jian-Xiu X Guo, Hong-Yu Y Zhang
    posted to folding-rate protein-structure by wouterboomsma on 2006-08-30 19:05:14 as **
  • Protein folding by zipping and assembly.
    Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992.
    by SB Ozkan, GA Wu, JD Chodera, KA Dill
    posted to protein-structure by wouterboomsma on 2007-07-30 09:15:33 as *** along with 3 people aqeel cdeane ARobson
  • A contact energy function considering residue hydrophobic environment and its application in protein fold recognition.
    Genomics Proteomics Bioinformatics, Vol. 3, No. 4. (November 2005), pp. 218-224.
    by MJ Duan, YH Zhou
    posted to energy-function protein-structure by wouterboomsma on 2006-07-24 14:46:30 as **
  • Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.
    Curr Opin Struct Biol (3 May 2006)
    by Rachel Kolodny, Donald Petrey, Barry Honig
    posted to protein-structure by wouterboomsma on 2006-05-09 13:40:49 as ** along with 3 people and 2 groups ana dgront Inchoate structural_bioinformatics Bioinformatics
  • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2006), NA.
    by Philip Bradley, David Baker
    posted to protein-structure sampling by wouterboomsma on 2006-10-16 17:03:45 as **
  • A knowledge-based scoring function based on residue triplets for protein structure prediction.
    Protein Eng Des Sel (13 March 2006)
    by Shing-Chung C Ngan, Michael T T Inouye, Ram Samudrala
    posted to energy-function protein-structure by wouterboomsma on 2006-04-10 10:01:34 as ** along with 1 person klo
  • LINUS: a hierarchic procedure to predict the fold of a protein.
    Proteins, Vol. 22, No. 2. (June 1995), pp. 81-99.
    by R Srinivasan, GD Rose
    posted to local-structure protein-structure by wouterboomsma on 2007-02-23 19:53:51 as read
  • Automated structure prediction of weakly homologous proteins on a genomic scale
    PNAS, Vol. 101, No. 20. (18 May 2004), pp. 7594-7599.
    by Yang Zhang, Jeffrey Skolnick
    posted to protein-structure by wouterboomsma on 2007-02-26 10:45:29 as read along with 3 people nigham j3xucite mirzazadeh
  • Servers for protein structure prediction.
    Curr Opin Struct Biol (16 March 2006)
    by Daniel Fischer
    posted to protein-structure servers by wouterboomsma on 2006-04-10 10:00:06 as ** along with 6 people kuhn chad_davis dgront schuylrp granujilla Jporci
  • Rigorous performance evaluation in protein structure modelling and implications for computational biology.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 453-458.
    by J Moult
    posted to casp protein-structure by wouterboomsma on 2006-04-10 09:46:52 as *** along with 2 people chad_davis cdeane
  • Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide Model
    J. Chem. Theory Comput. (18 April 2006)
    by V Tozzini, W Rocchia, JA Mccammon
    posted to protein-structure representation by wouterboomsma on 2006-04-19 17:47:08 as read
  • A coarse-grained protein force field for folding and structure prediction.
    Proteins (28 June 2007)
    by Julien Maupetit, P Tuffery, Philippe Derreumaux
    posted to energy-function protein-structure by wouterboomsma on 2007-07-09 10:54:21 as ** along with 1 person choonpeng
  • 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 secondary-structure by wouterboomsma on 2007-10-03 15:16:01 as ** along with 2 people thamelry j3xucite
  • Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study
    PNAS, Vol. 103, No. 9. (28 February 2006), pp. 3141-3146.
    by George Chikenji, Yoshimi Fujitsuka, Shoji Takada
    posted to fragments protein-structure by wouterboomsma on 2007-02-26 18:13:08 as read along with 3 people eckart_bindewald rsantana saunders
  • Protein structure prediction: Combining de novo modeling with sparse experimental data.
    J Comput Chem (6 March 2007)
    by Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski
    posted to experimental-data protein-structure by wouterboomsma on 2007-05-15 10:53:27 as **
  • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 209-225.
    by KT Simons, C Kooperberg, E Huang, D Baker
    posted to fragments protein-structure by wouterboomsma on 2005-11-17 12:22:10 as read along with 7 people and 2 groups ana jwm vavi j3xucite hmk mijam joule structural_bioinformatics Bioinformatics
  • Prediction of peptide structure: How far are we?
    Proteins (3 October 2006)
    by Annick Thomas, Sébastien Deshayes, Marc Decaffmeyer, Marie Hélène H Van Eyck, Benoit Charloteaux, Robert Brasseur
    posted to protein-structure review by wouterboomsma on 2006-10-09 07:33:28 as **
  • Protein secondary structure prediction based on position-specific scoring matrices.
    J Mol Biol, Vol. 292, No. 2. (17 September 1999), pp. 195-202.
    by DT Jones
    posted to protein-structure secondary-structure by wouterboomsma on 2007-09-05 12:57:13 as ** along with 9 people chad_davis j3xucite dgront leelarcombe rabio rph dandaman saunders granujilla
  • Determination of the conformation of folding initiation sites in proteins by computer simulation.
    Proteins, Vol. 23, No. 2. (October 1995), pp. 129-141.
    by F Avbelj, J Moult
    posted to protein-structure by wouterboomsma on 2007-02-26 11:57:08 as read
  • Prediction of local structure in proteins using a library of sequence-structure motifs.
    J Mol Biol, Vol. 281, No. 3. (21 August 1998), pp. 565-577.
    by C Bystroff, D Baker
    posted to fragments protein-structure by wouterboomsma on 2007-02-22 19:21:16 as read along with 1 person dgront
  • Dissecting contact potentials for proteins: Relative contributions of individual amino acids.
    Proteins (19 July 2007)
    by N-V V Buchete, J E E Straub, D Thirumalai
    posted to energy-function protein-structure by wouterboomsma on 2007-07-30 09:22:06 as ** along with 2 people RamuAnandakrishnan kgutwin
  • 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-structure representation by wouterboomsma on 2007-05-15 10:52:30 as ** along with 4 people j3xucite dgront sekmi mijam
  • Atom-wise statistics and prediction of solvent accessibility in proteins.
    Biophys Chem (20 July 2006)
    by Y Hemajit H Singh, M Michael M Gromiha, Akinori Sarai, Shandar Ahmad
    posted to protein-structure solvent-exposure by wouterboomsma on 2006-07-26 11:41:52 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 fragments protein-structure by wouterboomsma on 2007-02-27 14:03:55 as read along with 4 people and 1 group j3xucite dgront rabio wenhan MBLAB
  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637.
    by W Kabsch, C Sander
    posted to protein-structure secondary-structure by wouterboomsma on 2007-09-05 13:09:57 as ** along with 17 people Diego_Prada pjcite kaarsinogen lna chad_davis penka ffranca dgront choonpeng leelarcombe rabio gisle medic0747 martainn chgjb mschofie marti
  • Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo.
    J Chem Phys, Vol. 126, No. 22. (14 June 2007)
    by J Zhang, SC Kou, JS Liu
    posted to mcmc protein-structure by wouterboomsma on 2007-07-09 10:51:36 as ** along with 1 person huyun110
  • Modular DAG-RNN architectures for assembling coarse protein structures.
    J Comput Biol, Vol. 13, No. 3. (April 2006), pp. 631-650.
    by G Pollastri, A Vullo, P Frasconi, P Baldi
    posted to protein-structure representation by wouterboomsma on 2006-07-24 12:32:29 as **
  • Towards high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
    BMC Structural Biology, Vol. 7 (29 June 2007), 43.
    by Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski
    posted to protein-structure by wouterboomsma on 2007-07-09 10:56:24 as ** along with 2 people rabio sekmi
  • Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 353-366.
    by A Kolinski, J Skolnick
    posted to lattice protein-structure by wouterboomsma on 2007-02-26 17:33:07 as read
  • Protein structure prediction aided by geometrical and probabilistic constraints.
    J Comput Chem (20 April 2007)
    by Gaurav Porwal, Swapnil Jain, S Dhilly D Babu, Deepak Singh, Hemant Nanavati, Santosh Noronha
    posted to protein-structure by wouterboomsma on 2007-05-15 11:02:40 as **
  • Prediction of structures of multidomain proteins from structures of the individual domains.
    Protein Sci (22 December 2006)
    by Andrew M M Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker
    posted to protein-structure multi-domain by wouterboomsma on 2007-02-05 11:36:19 as ** along with 4 people choonpeng zwang IrinaMoreira rph
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