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carlks scp [51 articles]

Artikler nylig sendt til carlks bibliotek klassifisert med nøkkelordet scp. You can also see everyone's scp.
  • Modelling antibody side chain conformations using heuristic database search.
    Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (1997), pp. 237-240.
    by DW Ritchie, GJ Kemp
    posted to protein scp by carlk on 2008-06-30 14:48:34 as **
  • Excluded volume in protein side-chain packing.
    J Mol Biol, Vol. 311, No. 1. (3 August 2001), pp. 183-193.
    by E Kussell, J Shimada, EI Shakhnovich
    posted to energy protein scp structure by carlk on 2008-06-30 14:47:13 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Fitting protein chains to cubic lattice is NP-complete.
    Journal of bioinformatics and computational biology, Vol. 6, No. 1. (February 2008), pp. 93-106.
    by J Manuch, DR Gaur
    posted to lattice protein scp structure by carlk on 2008-06-26 19:05:51 as **
  • A Merge-Decoupling Dead End Elimination algorithm for protein side-chain conformation.
    International journal of data mining and bioinformatics, Vol. 1, No. 4. (2007), pp. 372-388.
    by KF Chong, HW Leong
    posted to algorithms protein scp structure by carlk on 2008-06-26 19:04:21 as **
  • Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains.
    Protein engineering, Vol. 8, No. 8. (August 1995), pp. 815-822.
    by I Lasters, M De Maeyer, J Desmet
    posted to algorithms protein scp structure by carlk on 2008-06-26 19:00:03 as **
  • A graph-theoretic algorithm for comparative modeling of protein structure.
    Journal of molecular biology, Vol. 279, No. 1. (29 May 1998), pp. 287-302.
    by R Samudrala, J Moult
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:59:24 as **
  • Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment.
    Journal of computational chemistry, Vol. 24, No. 15. (30 November 2003), pp. 1950-1961.
    by R Gautier, P Tufféry
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:59:10 as **
  • A new approach to the rapid determination of protein side chain conformations.
    J Biomol Struct Dyn, Vol. 8, No. 6. (June 1991), pp. 1267-1289.
    by P Tuffery, C Etchebest, S Hazout, R Lavery
    posted to algorithms historical protein scp structure by carlk on 2008-06-26 18:58:46 as * along with 1 person dgront
  • Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold.
    Journal of protein chemistry, Vol. 16, No. 5. (July 1997), pp. 449-452.
    by I Lasters, J Desmet, M De Maeyer
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:58:26 as **
  • Protein design automation.
    Protein Sci, Vol. 5, No. 5. (May 1996), pp. 895-903.
    by BI Dahiyat, SL Mayo
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:57:55 as ** along with 2 people and 1 group shuns nknii TCR_Signaling
  • A new pairwise folding potential based on improved decoy generation and side-chain packing.
    Proteins, Vol. 54, No. 2. (1 February 2004), pp. 303-314.
    by C Loose, JL Klepeis, CA Floudas
    posted to energy protein scp structure by carlk on 2008-06-26 18:57:20 as **
  • Prediction and evaluation of side-chain conformations for protein backbone structures.
    Proteins, Vol. 26, No. 3. (November 1996), pp. 323-352.
    by PS Shenkin, H Farid, JS Fetrow
    posted to algorithms historical protein scp structure by carlk on 2008-06-26 18:56:52 as **
  • Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.
    Biopolymers, Vol. 59, No. 2. (August 2001), pp. 72-86.
    by J Mendes, HA Nagarajaram, CM Soares, TL Blundell, MA Carrondo
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:56:29 as ** along with 1 person medic0747
  • Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm.
    Genome informatics. International Conference on Genome Informatics, Vol. 13 (2002), pp. 143-152.
    by BK Dukka, T Akutsu, E Tomita, T Seki, A Fujiyama
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:54:29 as **
  • Determinants of protein side-chain packing.
    Protein science : a publication of the Protein Society, Vol. 3, No. 12. (December 1994), pp. 2358-2365.
    by R Tanimura, A Kidera, H Nakamura
    posted to protein scp structure by carlk on 2008-06-26 18:53:48 as **
  • The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins.
    Protein science : a publication of the Protein Society, Vol. 4, No. 11. (November 1995), pp. 2300-2309.
    by SY Chung, S Subbiah
    posted to protein scp structure virus by carlk on 2008-06-26 18:52:59 as **
  • Analysis of side-chain rotamers in transmembrane proteins.
    Biophysical journal, Vol. 87, No. 5. (November 2004), pp. 3460-3469.
    by AK Chamberlain, JU Bowie
    posted to protein scp structure by carlk on 2008-06-26 18:51:26 as ** along with 1 person and 1 group xdeupi LabCompMed
  • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
    J Mol Biol, Vol. 267, No. 5. (18 April 1997), pp. 1268-1282.
    by MJ Bower, FE Cohen, RL Dunbrack
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:50:21 as ** along with 5 people and 1 group kaarsinogen nknii blackbart mijam jwm TCR_Signaling
  • 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 algorithms protein scp structure by carlk on 2008-06-26 18:50:04 as ** along with 9 people karbak nigham bicko blackbart bluvsh1 rsantana mijam jwm newton1234
  • A tree-decomposition approach to protein structure prediction.
    Proc IEEE Comput Syst Bioinform Conf (2005), pp. 247-256.
    by J Xu, F Jiao, B Berger
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:49:50 as **** along with 1 person j3xucite
  • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Ivelin Georgiev, Ryan H Lilien, Bruce R Donald
    posted to design protein scp structure by carlk on 2008-06-26 18:33:10 as ** along with 1 person RamuAnandakrishnan
  • Dead-end elimination for multistate protein design.
    Journal of computational chemistry, Vol. 28, No. 13. (October 2007), pp. 2122-2129.
    by C Yanover, M Fromer, JM Shifman
    posted to design protein scp structure by carlk on 2008-06-26 18:31:58 as **
  • Dead-end elimination with backbone flexibility.
    Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007)
    by I Georgiev, BR Donald
    posted to scp structure by carlk on 2008-06-26 18:31:28 as ****
  • Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design.
    Bioinformatics (Oxford, England), Vol. 22, No. 14. (15 July 2006)
    by I Georgiev, RH Lilien, BR Donald
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:29:07 as **
  • Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.
    Journal of bioinformatics and computational biology, Vol. 3, No. 1. (February 2005), pp. 103-126.
    by KC Dukka Bahadur, E Tomita, J Suzuki, T Akutsu
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:27:44 as **
  • 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 algorithms protein scp structure by carlk on 2008-06-26 18:26:40 as ***** along with 3 people and 2 groups bicko marcius bluvsh1 BioinfoCIPF SGU-CIPF
  • Exploring conformational space using a mean field technique with MOLS sampling.
    Journal of biosciences, Vol. 32, No. 5. (August 2007), pp. 909-920.
    by PA Prasad, V Kanagasabai, J Arunachalam, N Gautham
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:25:42 as *****
  • IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
    Protein science : a publication of the Protein Society, Vol. 16, No. 7. (July 2007), pp. 1294-1307.
    by C Hartmann, I Antes, T Lengauer
    posted to algorithms protein scp search structure by carlk on 2008-06-26 18:24:57 as **
  • Analysis of side-chain orientations in homologous proteins.
    J Mol Biol, Vol. 196, No. 1. (5 July 1987), pp. 175-198.
    by NL Summers, WD Carlson, M Karplus
    posted to scp structure by carlk on 2008-06-26 18:23:35 as ** along with 1 person blackbart
  • Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.
    J Mol Biol, Vol. 230, No. 2. (20 March 1993), pp. 592-612.
    by H Schrauber, F Eisenhaber, P Argos
    posted to protein scp structure by carlk on 2008-06-26 18:23:08 as ** along with 1 person blackbart
  • 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 algorithms protein scp structure by carlk on 2008-06-26 18:22:22 as ** along with 5 people dgront bluvsh1 kazemi rsantana mijam
  • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.
    Proteins, Vol. 26, No. 4. (December 1996), pp. 363-376.
    by RW Hooft, C Sander, G Vriend
    posted to scp structure by carlk on 2008-06-26 18:21:59 as **** along with 1 person lna
  • Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods.
    Proteins, Vol. 33, No. 2. (1 November 1998), pp. 204-217.
    by ES Huang, P Koehl, M Levitt, RV Pappu, JW Ponder
    posted to scp structure by carlk on 2008-06-26 18:21:17 as **
  • Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction.
    Proteins, Vol. 37, No. 1. (1 October 1999), pp. 30-43.
    by J Heringa, P Argos
    posted to scp structure by carlk on 2008-06-26 18:20:08 as ** along with 1 person blackbart
  • SCit: web tools for protein side chain conformation analysis.
    Nucleic acids research, Vol. 32, No. Web Server issue. (1 July 2004)
    by R Gautier, AC Camproux, P Tufféry
    posted to scp structure by carlk on 2008-06-26 18:19:27 as **
  • Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
    J Mol Biol, Vol. 230, No. 2. (20 March 1993), pp. 543-574.
    by RL Dunbrack, M Karplus
    posted to scp structure by carlk on 2008-06-26 16:39:20 as ** along with 1 person and 1 group nknii TCR_Signaling
  • The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem.
    Protein engineering, Vol. 6, No. 7. (September 1993), pp. 717-722.
    by I Lasters, J Desmet
    posted to algorithms scp structure by carlk on 2008-06-26 16:38:58 as **
  • Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.
    Proteins, Vol. 37, No. 4. (1 December 1999), pp. 530-543.
    by J Mendes, AM Baptista, MA Carrondo, CM Soares
    posted to scp structure by carlk on 2008-06-26 16:38:35 as ** along with 1 person blackbart
  • 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 comparison design scp structure by carlk on 2008-06-26 16:37:55 as ** along with 1 person bluvsh1
  • Automatic protein design with all atom force-fields by exact and heuristic optimization.
    Journal of molecular biology, Vol. 301, No. 3. (18 August 2000), pp. 713-736.
    by L Wernisch, S Hery, SJ Wodak
    posted to design scp structure by carlk on 2008-06-26 16:36:59 as **
  • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.
    J Mol Biol, Vol. 307, No. 1. (16 March 2001), pp. 429-445.
    by LL Looger, HW Hellinga
    posted to scp structure by carlk on 2008-06-26 16:36:27 as ** along with 3 people and 1 group nknii dgront mijam TCR_Signaling
  • FE: efficient molecular docking considering protein structure variations
    Journal of Molecular Biology, Vol. 308, No. 2. (27 April 2001), pp. 377-395.
    by Holger Clau[ss]en, Christian Buning, Matthias Rarey, Thomas Lengauer
    posted to docking scp structure by carlk on 2008-06-26 16:36:09 as ** along with 3 people apaydin blackbart kazemi
  • Modelling protein side-chain conformations using constraint logic programming.
    Comput Chem, Vol. 26, No. 1. (December 2001), pp. 85-95.
    by MT Swain, GJ Kemp
    posted to algorithms scp structure by carlk on 2008-06-26 16:35:24 as ** along with 1 person karbak
  • Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.
    Protein Sci, Vol. 13, No. 3. (March 2004), pp. 735-751.
    by RW Peterson, PL Dutton, AJ Wand
    posted to algorithms scp structure by carlk on 2008-06-26 16:34:51 as ** along with 2 people karbak blackbart
  • 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 algorithms scp structure by carlk on 2008-06-26 16:31:49 as ** along with 2 people apaydin bluvsh1
  • Protein folding: the endgame.
    Annual review of biochemistry, Vol. 66 (1997), pp. 549-579.
    by M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai
    posted to review scp structure by carlk on 2008-06-26 16:21:29 as **
  • Side chain substitution benchmark for peptide/MHC interaction.
    Protein science : a publication of the Protein Society, Vol. 17, No. 6. (June 2008), pp. 977-982.
    by B Knapp, U Omasits, W Schreiner
    posted to scp structure by carlk on 2008-06-26 16:20:59 as ****
  • Andante: Reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.
    Bioinformatics (6 March 2007)
    by Richard E E Smith, Simon C C Lovell, David F F Burke, Rinaldo W W Montalvao, Tom L L Blundell
    posted to scp structure by carlk on 2008-06-26 16:20:16 as ** along with 1 person jwm
  • Combinatorial methods for small-molecule placement in computational enzyme design.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 45. (7 November 2006), pp. 16710-16715.
    by JK Lassila, HK Privett, BD Allen, SL Mayo
    posted to design scp structure by carlk on 2008-06-26 16:19:43 as **
  • Side chain placement using estimation of distribution algorithms
    Artificial Intelligence in Medicine, Vol. 39, No. 1. (January 2007), pp. 49-63.
    by Roberto Santana, Pedro Larranaga, Jose A Lozano
    posted to scp structure by carlk on 2008-06-26 16:19:08 as ** along with 2 people rsantana mijam
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