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carlks structure [58 articles]

Senaste hänvisningarna i carlks bibliotek insorterade under taggen structure. You can also see everyone's structure.
  • 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 structure scp protein energy 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 structure scp protein lattice 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein historical algorithms 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 structure scp protein energy algorithms 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 structure scp protein energy algorithms 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 structure scp protein energy 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 structure scp protein historical algorithms 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein 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 virus structure scp protein 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 structure scp protein 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 structure scp protein algorithms by carlk on 2008-06-26 18:50:21 as ** along with 5 people and 1 group jwm kaarsinogen nknii blackbart mijam 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 structure scp protein algorithms by carlk on 2008-06-26 18:50:04 as ** along with 9 people newton1234 jwm karbak nigham bicko blackbart bluvsh1 rsantana mijam
  • 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 structure scp protein algorithms by carlk on 2008-06-26 18:49:50 as **** along with 1 person j3xucite
  • 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 27-52.
    by A Caprara, R Carr, S Istrail, G Lancia, B Walenz
    posted to structure protein alignment by carlk on 2008-06-26 18:34:32 as ** along with 2 people and 2 groups ana vavi structural_bioinformatics Bioinformatics
  • 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 structure scp protein design 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 structure scp protein design 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 structure scp by carlk on 2008-06-26 18:31:28 as ****
  • A reduction-based exact algorithm for the contact map overlap problem.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 5. (June 2007), pp. 637-654.
    by W Xie, NV Sahinidis
    posted to structure protein alignment by carlk on 2008-06-26 18:30:29 as **
  • Matt: Local Flexibility Aids Protein Multiple Structure Alignment.
    PLoS Comput Biol, Vol. 4, No. 1. (11 January 2008)
    by Matthew Menke, Bonnie Berger, Lenore Cowen
    posted to structure alignment by carlk on 2008-06-26 18:29:44 as ** along with 2 people dimka marti
  • 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein algorithms 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 structure scp protein energy algorithms 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 structure search scp protein algorithms 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 structure scp 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 structure scp protein 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 structure scp protein algorithms 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 structure scp 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 structure scp by carlk on 2008-06-26 18:21:17 as **
  • Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers.
    Proteins, Vol. 32, No. 2. (1 August 1998), pp. 159-174.
    by B Sandak, HJ Wolfson, R Nussinov
    posted to structure docking by carlk on 2008-06-26 18:20:39 as ** along with 1 person blackbart
  • 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 structure scp 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 structure scp 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 structure scp 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 structure scp algorithms 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 structure scp 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 structure scp design comparison 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 structure scp design 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 structure scp 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 structure scp docking 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 structure scp algorithms 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 structure scp algorithms 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 structure scp algorithms 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 structure scp review 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 structure scp by carlk on 2008-06-26 16:20:59 as ****
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