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newton1234s library [97 articles]

Senaste artiklarna i newton1234s bibliotek.
  • Numerical Recipes: The Art of Scientific Computing
    (1992)
    by William H Press, Saul A Teukolsky, William T Vetterling, Brian P Flannery
    posted to book by newton1234 on 2008-07-16 18:22:35 as **
  • Improving the quality of protein structure models by selecting from alignment alternatives
    BMC Bioinformatics, Vol. 7 (27 July 2006), 364.
    by Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer, Silvio CE Tosatto
    posted to optimization alignment by newton1234 on 2008-07-16 09:54:30 as **
  • Comparative protein structure modeling by iterative alignment, model building and model assessment
    Nucl. Acids Res., Vol. 31, No. 14. (15 July 2003), pp. 3982-3992.
    by Bino John, Andrej Sali
    posted to optimization modeller alignment by newton1234 on 2008-07-16 09:08:40 as **
  • 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 sidechain by newton1234 on 2008-07-16 09:05:13 as ** along with 9 people carlk jwm karbak nigham bicko blackbart bluvsh1 rsantana mijam
  • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    Proceedings of the National Academy of Sciences, Vol. 93, No. 22. (29 October 1996), pp. 12098-12103.
    by Burkhard Morgenstern, Andreas Dress, Thomas Werner
    posted to msa alignment by newton1234 on 2008-06-25 17:11:36 as ** along with 2 people adijr gjuggler
  • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.
    Journal of molecular biology, Vol. 264, No. 4. (13 December 1996), pp. 823-838.
    by O Gotoh
    posted to alignment by newton1234 on 2008-06-25 17:08:12 as **
  • A Template-based Mixed-Integer Linear Programming Sequence Alignment Model.
    (2007)
    by SR Mcallister, R Rajgaria, CA Floudas
    edited by T Torn, J Zilinskas
    posted to optimization alignment by newton1234 on 2008-06-25 16:52:59 as **
  • Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach
    Optimization Methods and Software, Vol. 22, No. 1. (2007), pp. 127-144.
    by SR Mcallister, R Rajgaria, CA Floudas
    posted to optimization alignment by newton1234 on 2008-06-25 16:18:27 as **
  • A path selection approach to global pairwise sequence alignment using integer linear optimization
    Optimization, Vol. 57, No. 1. (2008), pp. 101-111.
    by SR Mcallister, R Rajgaria, CA Floudas
    posted to optimization alignment by newton1234 on 2008-06-25 16:16:04 as **
  • A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.
    Proteins, Vol. 65, No. 3. (15 November 2006), pp. 726-741.
    by R Rajgaria, SR McAllister, CA Floudas
    posted to forcefield by newton1234 on 2008-06-25 16:12:21 as **
  • Assessment of CASP7 predictions in the high accuracy template-based modeling category.
    Proteins, Vol. 69 Suppl 8 (2007), pp. 27-37.
    by RJ Read, G Chavali
    posted to tbm hatbm by newton1234 on 2008-06-18 09:55:38 as **
  • High accuracy template based modeling by global optimization
    Proteins, Vol. 69 Suppl 8, No. 9999. (2007), pp. 83-89.
    by Keehyoung Joo, Jinwoo Lee, Sunjoong Lee, Joo-Hyun Seo, Sung J Lee, Jooyoung Lee
    posted to optimization csa by newton1234 on 2008-06-18 09:52:08 as ** along with 1 person r2s2
  • Ground-state energy and energy landscape of the Sherrington-Kirkpatrick spin glass
    Phys. Rev. B, Vol. 76, No. 18. (2007), 184412.
    by Seung Y Kim, Sung J Lee, Jooyoung Lee
    posted to optimization csa by newton1234 on 2008-06-18 09:50:22 as **
  • Vortex patterns and infinite degeneracy in the uniformly frustrated XY models and lattice Coulomb gas
    Phys. Rev. E, Vol. 67, No. 4. (2003)
    by Myoung K Ko, Sung J Lee, Jooyoung Lee, Bongsoo Kim
    posted to optimization by newton1234 on 2008-06-18 09:41:35 as **
  • Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
    Proc. Natl. Acad. Sci., Vol. 84, No. 19. (October 1987), pp. 6611-6615.
    by Z Li, HA Scheraga
    posted to optimization by newton1234 on 2008-06-18 09:38:03 as ** along with 1 person dgront
  • Genetic Algorithms in Search, Optimization, and Machine Learning
    (1989)
    by David E Goldberg
    posted to optimization by newton1234 on 2008-06-18 09:35:01 as **
  • PROMALS: towards accurate multiple sequence alignments of distantly related proteins
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 802-808.
    by Pei, Jimin, Grishin, V Nick
    posted to msa alignment by newton1234 on 2008-06-17 23:16:16 as **
  • HOMSTRAD: a database of protein structure alignments for homologous families.
    Protein Sci., Vol. 7, No. 11. (November 1998), pp. 2469-2471.
    by K Mizuguchi, CM Deane, TL Blundell, JP Overington
    posted to msa alignment by newton1234 on 2008-06-17 23:13:01 as ** along with 5 people chrn massivemayhem medic0747 cdeane sebk
  • BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
    Bioinformatics, Vol. 15, No. 1. (1 January 1999), pp. 87-88.
    by Jd Thompson, F Plewniak, O Poch
    posted to msa alignment by newton1234 on 2008-06-17 23:10:26 as ** along with 1 person BioNica
  • Simultaneous comparison of three protein sequences.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 10. (May 1985), pp. 3073-3077.
    by M Murata, JS Richardson, JL Sussman
    posted to alignment by newton1234 on 2008-06-17 23:08:20 as **
  • Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.
    Trends Biochem Sci, Vol. 23, No. 11. (November 1998), pp. 444-447.
    by SF Altschul, EV Koonin
    posted to alignment by newton1234 on 2008-06-17 23:05:45 as ** along with 1 person chad_davis
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res., Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to alignment by newton1234 on 2008-06-17 23:04:47 as ** along with 44 people and 4 groups CharlesM marti granujilla david_parsons edvin bandrewfox mariakmejia knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
    Int. J. Quantum Chem., Vol. 77, No. 1. (2000), pp. 90-117.
    by Jooyoung Lee, Adam Liwo, Daniel R Ripoll, Jaroslaw Pillardy, Jeffrey A Saunders, Kenneth D Gibson, Harold A Scheraga
    posted to csa by newton1234 on 2008-06-17 23:01:25 as **
  • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing.
    Proteins, Vol. 56, No. 4. (1 September 2004), pp. 704-714.
    by J Lee, SY Kim, K Joo, I Kim, J Lee
    posted to optimization csa by newton1234 on 2008-06-17 22:55:43 as **
  • Genetic algorithms and the optimal allocations of trials
    SIAM Journal of Computing, Vol. 2 (1973), pp. 88-105.
    by J Holland
    posted to optimization by newton1234 on 2008-06-17 22:54:33 as **
  • Simulated Annealing: Theory and Applications
    (1992)
    by Peter JM Laarhoven, Emile HL Aarts
    posted to book by newton1234 on 2008-06-17 21:50:20 as **
  • Optimization by Simulated Annealing
    Science, Vol. 220, No. 4598. (13 May 1983), pp. 671-680.
    by S Kirkpatrick, CD Gelatt, MP Vecchi
    posted to optimization by newton1234 on 2008-06-17 21:41:38 as ** along with 4 people ywlin ddahlem Bc91 naegele
  • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    Proc. Natl. Acad. Sci., Vol. 96, No. 5. (2 March 1999), pp. 2025-2030.
    by Jooyoung Lee, Adam Liwo, Harold A Scheraga
    posted to optimization csa by newton1234 on 2008-06-17 21:39:17 as **
  • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing.
    Biopolymers, Vol. 46, No. 2. (August 1998), pp. 103-116.
    by J Lee, HA Scheraga, S Rackovsky
    posted to optimization csa by newton1234 on 2008-06-17 21:37:56 as ** along with 1 person psi
  • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    J. Comput. Chem., Vol. 18, No. 9. (1997), pp. 1222-1232.
    by Jooyoung Lee, Harold A Scheraga, S Rackovsky
    posted to optimization csa by newton1234 on 2008-06-17 21:35:24 as ** along with 1 person dgront
  • A novel randomized iterative strategy for aligning multiple protein sequences.
    Computer applications in the biosciences : CABIOS, Vol. 7, No. 4. (October 1991), pp. 479-484.
    by MP Berger, PJ Munson
    posted to msa alignment by newton1234 on 2008-06-17 21:25:22 as **
  • ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res., Vol. 15, No. 2. (February 2005), pp. 330-340.
    by CB Do, MS Mahabhashyam, M Brudno, S Batzoglou
    posted to msa alignment by newton1234 on 2008-06-17 21:24:26 as ** along with 6 people and 1 group gjuggler bpb radek balajis stajich olympos Berkeley Mycology
  • SAGA: sequence alignment by genetic algorithm.
    Nucleic Acids Res., Vol. 24, No. 8. (15 April 1996), pp. 1515-1524.
    by C Notredame, DG Higgins
    posted to msa alignment by newton1234 on 2008-06-17 21:23:30 as **
  • Simulated annealing algorithm for the multiple sequence alignment problem: the approach of polymers in a random medium.
    Phys. Rev. E, Vol. 72, No. 3 Pt 1. (September 2005), 031915.
    by M Hernández-Guía, R Mulet, S Rodríguez-Pérez
    posted to msa alignment by newton1234 on 2008-06-17 21:22:43 as **
  • Multiple sequence alignment using simulated annealing
    CABIOS, Vol. 10, No. 4. (1 July 1994), pp. 419-426.
    by Jin Kim, Sakti Pramanik, Moon J Chung
    posted to msa alignment by newton1234 on 2008-06-17 21:20:47 as **
  • Multiple sequence alignment by parallel simulated annealing.
    CABIOS, Vol. 9, No. 3. (June 1993), pp. 267-273.
    by M Ishikawa, T Toya, M Hoshida, K Nitta, A Ogiwara, M Kanehisa
    posted to msa alignment by newton1234 on 2008-06-17 21:18:18 as **
  • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.
    Proteins, Vol. 58, No. 2. (1 February 2005), pp. 321-328.
    by H Zhou, Y Zhou
    posted to msa alignment by newton1234 on 2008-06-17 21:17:33 as **
  • SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3615-3621.
    by H Zhou, Y Zhou
    posted to msa alignment by newton1234 on 2008-06-17 21:16:06 as **
  • T-Coffee: A novel method for fast and accurate multiple sequence alignment.
    J. Mol. Biol., Vol. 302, No. 1. (8 September 2000), pp. 205-217.
    by C Notredame, DG Higgins, J Heringa
    posted to msa alignment by newton1234 on 2008-06-17 21:14:35 as ** along with 9 people and 1 group miguel dayjm indigoviolet ffranca treangen Haggan siebertm adijr marti EisenLab
  • MUSCLE: multiple sequence alignment with high accuracy and high throughput.
    Nucleic Acids Res., Vol. 32, No. 5. (2004), pp. 1792-1797.
    by RC Edgar
    posted to msa alignment by newton1234 on 2008-06-17 21:13:52 as ** along with 15 people and 2 groups dmp kcrawlik sconlan skumagai edvin sanchezbuelna bmaust nachtalp bpb chrn jwm Haggan timflutre olympos martainn Radiation_Damage Stressosome
  • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res., Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.
    by JD Thompson, DG Higgins, TJ Gibson
    posted to msa alignment by newton1234 on 2008-06-17 21:12:55 as ** along with 23 people and 1 group Lombardo_7 jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica leelarcombe timflutre adijr xingxu biomedical-nlp
  • Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
    J. Mol. Evol., Vol. 25, No. 4. (1987), pp. 351-360.
    by DF Feng, RF Doolittle
    posted to msa alignment by newton1234 on 2008-06-17 21:12:10 as ** along with 3 people balajis nuke2005 AaronDarling
  • Identification of common molecular subsequences.
    J. Mol. Biol., Vol. 147, No. 1. (25 March 1981), pp. 195-197.
    by TF Smith, MS Waterman
    posted to alignment by newton1234 on 2008-06-17 21:10:48 as ** along with 9 people bozdagd creswick vavi bicko dgront rabio cjeans incovoma sujaikumar
  • A general method applicable to the search for similarities in the amino acid sequence of two proteins.
    J. Mol. Biol., Vol. 48, No. 3. (March 1970), pp. 443-453.
    by SB Needleman, CD Wunsch
    posted to alignment by newton1234 on 2008-06-17 21:09:17 as ** along with 6 people Ema yylin jwm dgront rabio incovoma
  • The multiple sequence alignment problem in biology
    SIAM J. Appl. Math., Vol. 48, No. 5. (1988), pp. 1073-1082.
    by Humberto Carrillo, David Lipman
    posted to msa alignment by newton1234 on 2008-06-17 21:08:12 as **
  • On the complexity of multiple sequence alignment.
    J. Comput. Biol., Vol. 1, No. 4. (1994), pp. 337-348.
    by L Wang, T Jiang
    posted to msa alignment by newton1234 on 2008-06-17 21:03:46 as ** along with 2 people yylin treangen
  • COFFEE: an objective function for multiple sequence alignments.
    Bioinformatics, Vol. 14, No. 5. (June 1998), pp. 407-422.
    by C Notredame, L Holm, DG Higgins
    posted to msa alignment by newton1234 on 2008-06-17 21:02:50 as **
  • Weights for data related by a tree.
    J. Mol. Biol., Vol. 207, No. 4. (20 June 1989), pp. 647-653.
    by SF Altschul, RJ Carroll, DJ Lipman
    posted to msa alignment by newton1234 on 2008-06-17 21:01:51 as ** along with 1 person nuke2005
  • Gap costs for multiple sequence alignment.
    Journal of theoretical biology, Vol. 138, No. 3. (8 June 1989), pp. 297-309.
    by SF Altschul
    posted to msa alignment by newton1234 on 2008-06-17 21:00:38 as **
  • Recent progress in multiple sequence alignment: a survey.
    Pharmacogenomics, Vol. 3, No. 1. (January 2002), pp. 131-144.
    by C Notredame
    posted to msa alignment by newton1234 on 2008-06-17 20:58:54 as **
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