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bluvsh1 library [39 articles]

Статьи, недавно добавленные в библиотеку bluvsh1 .
  • Efficient rotamer elimination applied to protein side-chains and related spin glasses.
    Biophys J, Vol. 66, No. 5. (May 1994), pp. 1335-1340.
    by RF Goldstein
    posted to scp by bluvsh1 on 2006-04-26 13:38:15 as * along with 5 people dgront kazemi rsantana mijam carlk
  • The dead-end elimination theorem and its use in protein side-chain positioning
    Nature, Vol. 356, No. 6369. (April 1992), pp. 539-542.
    by Johan Desmet, , Marc D Maeyer, Bart Hazes, Ignace Lasters
    posted to scp by bluvsh1 on 2006-04-26 13:18:41 as read along with 2 people dgront mijam
  • A semidefinite programming approach to side-chain positioning with new rounding strategies
    INFORMS J. Comput., Vol. 16 (2004), pp. 380-392.
    by B Chazelle, C Kingsford, M Singh
    posted to scp by bluvsh1 on 2006-04-26 13:14:22 as **
  • Protein Design is NP-hard
    Protein Eng., Vol. 15, No. 10. (1 October 2002), pp. 779-782.
    by Niles A Pierce, Erik Winfree
    posted to scp by bluvsh1 on 2006-04-26 13:09:37 as * along with 6 people ansobol ima gane5h kray mijam iantunbridge
  • High-resolution protein-protein docking
    Current Opinion in Structural Biology, Vol. 16, No. 2. (April 2006), pp. 183-193.
    by Jeffrey J Gray
    posted to methods by bluvsh1 on 2006-04-25 17:48:06 as *** along with 6 people aqeel jwm ima ruvido cjeans higueruelo
  • Determination of atomic desolvation energies from the structures of crystallized proteins.
    J Mol Biol, Vol. 267, No. 3. (4 April 1997), pp. 707-726.
    by C Zhang, G Vasmatzis, JL Cornette, C DeLisi
    posted to energy by bluvsh1 on 2006-04-25 17:44:31 as read along with 3 people ras ffranca GermanErlenkamp
  • Computational protein design is a challenge for implicit solvation models.
    Biophys J, Vol. 88, No. 1. (January 2005), pp. 156-171.
    by A Jaramillo, SJ Wodak
    posted to energy by bluvsh1 on 2006-04-25 17:43:41 as read
  • Anchor residues in protein-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 101, No. 31. (3 August 2004), pp. 11287-11292.
    by D Rajamani, S Thiel, S Vajda, CJ Camacho
    posted to bound_unbound by bluvsh1 on 2006-04-25 17:41:49 as read along with 3 people and 2 groups barry bicko boris_aguilar structural_bioinformatics Bioinformatics
  • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
    J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795.
    by X Li, O Keskin, B Ma, R Nussinov, J Liang
    posted to bound_unbound by bluvsh1 on 2006-04-25 17:37:37 as read along with 10 people and 2 groups barry baaden bicko nickolay j3xucite xz grahamc Evangelia ladab paolomarcatili structural_bioinformatics Bioinformatics
  • Effective energy function for proteins in solution.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152.
    by T Lazaridis, M Karplus
    posted to energy by bluvsh1 on 2006-04-25 17:36:28 as read along with 4 people and 2 groups marcius choonpeng hmk kgutwin BioinfoCIPF SGU-CIPF
  • Discrimination of the native from misfolded protein models with an energy function including implicit solvation.
    J Mol Biol, Vol. 288, No. 3. (7 May 1999), pp. 477-487.
    by T Lazaridis, M Karplus
    posted to energy by bluvsh1 on 2006-04-25 17:35:33 as read
  • An adaptive dynamic programming algorithm for the side chain placement problem.
    Pac Symp Biocomput (2005), pp. 16-27.
    by A Leaver-Fay, B Kuhlman, J Snoeyink
    posted to scp by bluvsh1 on 2006-04-25 17:33:16 as read along with 2 people apaydin carlk
  • Solving and analyzing side-chain positioning problems using linear and integer programming
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1028-1039.
    by L Kingsford, Chazelle Bernard, Singh Mona
    posted to scp by bluvsh1 on 2006-04-25 17:32:25 as read
  • Rapid Protein Side-Chain Packing via Tree Decomposition
    Lecture Notes in Computer Science, Vol. 3500 (January 2005), pp. 423-439.
    by J Xu
    posted to scp by bluvsh1 on 2006-04-25 17:31:06 as read
  • A combinatorial approach to protein docking with flexible side chains.
    J Comput Biol, Vol. 9, No. 4. (2002), pp. 597-612.
    by E Althaus, O Kohlbacher, HP Lenhof, P Müller
    posted to scp by bluvsh1 on 2006-04-25 17:24:11 as read
  • Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
    (2004), pp. 191-200.
    by Dukka KC Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki
    posted to scp by bluvsh1 on 2006-04-25 17:23:26 as read
  • Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design.
    J Mol Biol, Vol. 299, No. 3. (9 June 2000), pp. 789-803.
    by CA Voigt, DB Gordon, SL Mayo
    posted to scp by bluvsh1 on 2006-04-25 17:21:18 as read along with 1 person carlk
  • Branch-and-terminate: a combinatorial optimization algorithm for protein design.
    Structure, Vol. 7, No. 9. (15 September 1999), pp. 1089-1098.
    by DB Gordon, SL Mayo
    posted to scp by bluvsh1 on 2006-04-25 17:20:26 as read along with 1 person ima
  • A graph-theory algorithm for rapid protein side-chain prediction.
    Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2001-2014.
    by AA Canutescu, AA Shelenkov, RL Dunbrack
    posted to scp by bluvsh1 on 2006-04-25 17:19:46 as read along with 9 people karbak nigham bicko blackbart rsantana mijam jwm carlk newton1234
  • Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 188-194.
    by Wei Xie, Nikolaos V Sahinidis
    posted to scp by bluvsh1 on 2006-04-25 17:18:53 as read along with 3 people and 2 groups bicko marcius carlk BioinfoCIPF SGU-CIPF
  • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.
    J Mol Biol, Vol. 239, No. 2. (3 June 1994), pp. 249-275.
    by P Koehl, M Delarue
    posted to scp by bluvsh1 on 2006-04-25 17:17:31 as read
  • Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
    J Mol Biol, Vol. 276, No. 1. (13 February 1998), pp. 265-285.
    by RM Jackson, HA Gabb, MJ Sternberg
    posted to methods by bluvsh1 on 2006-04-25 17:14:51 as read
  • Exact rotamer optimization for protein design.
    J Comput Chem, Vol. 24, No. 2. (30 January 2003), pp. 232-243.
    by DB Gordon, GK Hom, SL Mayo, NA Pierce
    posted to scp by bluvsh1 on 2006-04-25 17:13:53 as read along with 1 person rsantana
  • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 150-169.
    by R Méndez, R Leplae, MF Lensink, SJ Wodak
    posted to capri by bluvsh1 on 2006-04-25 17:12:47 as read along with 1 person chad_davis
  • Protein-protein docking with a reduced protein model accounting for side-chain flexibility.
    Protein Sci, Vol. 12, No. 6. (June 2003), pp. 1271-1282.
    by M Zacharias
    posted to methods by bluvsh1 on 2006-04-25 17:12:05 as read along with 2 people blackbart choonpeng
  • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
    J Am Chem Soc, Vol. 125, No. 7. (19 February 2003), pp. 1731-1737.
    by C Dominguez, R Boelens, AM Bonvin
    posted to methods by bluvsh1 on 2006-04-25 17:10:36 as read along with 6 people betainverse dgruiz bicko gloria ruvido yalexeev
  • Screened charge electrostatic model in protein-protein docking simulations.
    Pac Symp Biocomput (2002), pp. 552-563.
    by J Fernandez-Recio, M Totrov, R Abagyan
    posted to energy by bluvsh1 on 2006-04-25 17:08:37 as read
  • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
    J Mol Biol, Vol. 235, No. 3. (21 January 1994), pp. 983-1002.
    by R Abagyan, M Totrov
    posted to methods by bluvsh1 on 2006-04-25 17:07:45 as read along with 2 people RamuAnandakrishnan sigalov
  • Identification of protein-protein interaction sites from docking energy landscapes.
    J Mol Biol, Vol. 335, No. 3. (16 January 2004), pp. 843-865.
    by J Fernández-Recio, M Totrov, R Abagyan
    posted to methods by bluvsh1 on 2006-04-25 17:05:49 as read
  • Soft protein-protein docking in internal coordinates.
    Protein Sci, Vol. 11, No. 2. (February 2002), pp. 280-291.
    by J Fernández-Recio, M Totrov, R Abagyan
    posted to methods by bluvsh1 on 2006-04-25 17:04:56 as read along with 5 people and 2 groups barry bicko cjeans selrac wilbur structural_bioinformatics Bioinformatics
  • ICM-DISCO docking by global energy optimization with fully flexible side-chains.
    Proteins, Vol. 52, No. 1. (1 July 2003), pp. 113-117.
    by J Fernández-Recio, M Totrov, R Abagyan
    posted to methods by bluvsh1 on 2006-04-25 17:04:05 as read along with 2 people bicko kazemi
  • Successful discrimination of protein interactions.
    Proteins, Vol. 52, No. 1. (1 July 2003), pp. 92-97.
    by CJ Camacho, DW Gatchell
    posted to methods by bluvsh1 on 2006-04-25 17:03:26 as read
  • Progress and challenges in high-resolution refinement of protein structure models.
    Proteins, Vol. 59, No. 1. (1 April 2005), pp. 15-29.
    by KM Misura, D Baker
    posted to methods by bluvsh1 on 2006-04-25 17:02:06 as ** along with 1 person insectopalo
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to methods by bluvsh1 on 2006-04-25 17:00:28 as read along with 9 people and 3 groups barry aqeel jwm bicko yongzhao blackbart hmk selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to methods by bluvsh1 on 2006-04-25 16:57:34 as read along with 3 people and 2 groups barry jwm bicko structural_bioinformatics Bioinformatics
  • RDOCK: refinement of rigid-body protein docking predictions
    Proteins, Vol. 53, No. 3. (2003), pp. 693-707.
    by L Li, R Chen, Z Weng
    posted to methods by bluvsh1 on 2006-04-25 16:48:04 as read
  • Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
    Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by Jeffrey J Gray, Stewart Moughon, Chu Wang, Ora Schueler-Furman, Brian Kuhlman, Carol A Rohl, David Baker
    posted to methods by bluvsh1 on 2006-04-25 16:40:13 as read along with 4 people xdeupi ima selrac timg
  • Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.
    Proteins, Vol. 52, No. 1. (1 July 2003), pp. 98-106.
    by DW Ritchie
    posted to methods by bluvsh1 on 2006-04-25 16:30:50 as read along with 1 person and 3 groups beapen Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
  • Protein-Protein Docking Benchmark 2.0: an update.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 214-216.
    by J Mintseris, K Wiehe, B Pierce, R Anderson, R Chen, J Janin, Z Weng
    posted to benchmarks by bluvsh1 on 2006-04-25 16:23:26 as read along with 9 people marti aqeel julianm bicko chad_davis ima selrac Iainios boris_aguilar
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