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marcius's algorithms [56 articles]

当前文献位于 marcius's 文献库 标签分类为 algorithms. You can also see everyone's algorithms.
  • The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
    Nucleic Acids Res (25 May 2007)
    by Sebastien Moretti, Fabrice Armougom, Iain M M Wallace, Desmond G G Higgins, Cornelius V V Jongeneel, Cedric Notredame
    posted to algorithms alignment sequence sequence_alignment by marcius on 2007-06-04 10:12:59 as ** along with 2 people and 2 groups sebastien_vigneau marti BioinfoCIPF SGU-CIPF
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to protein_domains evolution bioinformatics algorithms by marcius on 2007-01-25 08:31:09 as ** along with 6 people and 3 groups jameswasmuth icases tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
  • An RNA folding algorithm including pseudoknots based on dynamic weighted matching.
    Comput Biol Chem, Vol. 30, No. 1. (February 2006), pp. 72-76.
    by H Liu, D Xu, J Shao, Y Wang
    posted to algorithms rna secondary_structure by marcius on 2006-11-16 17:44:25 as ** along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
  • ProteinRNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
    Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2746-2752.
    by N Morozova, J Allers, Y Shamoo
    posted to bioinformatics protein_interactions rna algorithms by marcius on 2006-11-16 09:29:09 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Three-dimensional comparative modeling of RNA.
    Nucleic Acids Symp Ser, No. 36. (1997), pp. 69-71.
    by C Zwieb, F Müller
    posted to algorithms bioinformatics comparative_modeling rna by marcius on 2006-10-27 21:31:25 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • From The Cover: Global mapping of the protein structure space and application in structure-based inference of protein function
    PNAS, Vol. 102, No. 10. (8 March 2005), pp. 3651-3656.
    by Jingtong Hou, Se-Ran Jun, Chao Zhang, Sung-Hou Kim
    posted to algorithms bioinformatics clustering protein_structure by marcius on 2006-10-26 08:42:48 as ** along with 1 person and 2 groups tny BioinfoCIPF SGU-CIPF
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. e112-e112.
    by D Chivian, D Baker
    posted to algorithms bioinformatics comparative_modeling sequence_alignment by marcius on 2006-10-25 21:43:08 as ** along with 1 person and 2 groups j3xucite BioinfoCIPF SGU-CIPF
  • Protein–Protein Interactions More Conserved within Species than across Species
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e79.
    by Sven Mika, Burkhard Rost
    posted to algorithms evolution protein_domains protein_interactions by marcius on 2006-10-22 12:13:05 as ** along with 4 people and 2 groups jeremymiller chad_davis skhadar dquest BioinfoCIPF SGU-CIPF
  • Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
    PLoS Computational Biology, Vol. preprint, No. 2006. (1 October 2006)
    by Dmitry Korkin, Fred P Davis, Frank Alber, Tinh Luong, Min-Yi Shen, Vladan Lucic, Mary B Kennedy, Andrej Sali
    posted to algorithms comparative_docking comparative_modeling protein_domains protein_interactions by marcius on 2006-10-22 12:12:40 as ** along with 1 person and 2 groups bicko BioinfoCIPF SGU-CIPF
  • The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e124.
    by Wan K Kim, Andreas Henschel, Christof Winter, Michael Schroeder
    posted to algorithms databases protein_domains protein_interactions by marcius on 2006-10-22 12:12:00 as ** along with 9 people and 2 groups zdai raik bicko chad_davis choonpeng Evangelia wilbur allmensch marck BioinfoCIPF SGU-CIPF
  • Evaluation of library ranking efficacy in virtual screening.
    J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 11-22.
    by M Kontoyianni, GS Sokol, LM McClellan
    posted to algorithms docking drug ligand protein by marcius on 2006-10-21 14:25:23 as ** along with 3 people and 2 groups BragilMassoud nachtalp schuwi BioinfoCIPF SGU-CIPF
  • Virtual screening in structure-based drug discovery.
    Mini Rev Med Chem, Vol. 4, No. 7. (September 2004), pp. 779-791.
    by X Barril, RE Hubbard, SD Morley
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:22:35 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Virtual screening in lead discovery and optimization.
    Curr Opin Drug Discov Devel, Vol. 7, No. 4. (July 2004), pp. 396-403.
    by AN Jain
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:21:52 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Docking and scoring in virtual screening for drug discovery: methods and applications.
    Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949.
    by DB Kitchen, H Decornez, JR Furr, J Bajorath
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:16:46 as ** along with 6 people and 9 groups BragilMassoud dgruiz beapen anita yongzhao sangeetha Bioinformatics structure-bii TSRI_MGL Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
  • Current status of virtual screening as analysed by target class.
    Med Chem, Vol. 2, No. 1. (January 2006), pp. 89-112.
    by MJ Stoermer
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:14:08 as ** along with 1 person and 3 groups yongzhao TSRI_MGL BioinfoCIPF SGU-CIPF
  • Recent development and application of virtual screening in drug discovery: an overview.
    Curr Pharm Des, Vol. 10, No. 9. (2004), pp. 1011-1033.
    by T Hou, X Xu
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:12:44 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • A review of protein-small molecule docking methods.
    J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166.
    by RD Taylor, PJ Jewsbury, JW Essex
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:11:15 as ** along with 3 people and 4 groups sangeetha schlauchi massivemayhem Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
  • Computational tools for protein modeling.
    Curr Protein Pept Sci, Vol. 1, No. 1. (July 2000), pp. 1-21.
    by D Xu, Y Xu, EC Uberbacher
    posted to algorithms protein review by marcius on 2006-10-21 14:10:31 as ** along with 1 person and 2 groups granujilla BioinfoCIPF SGU-CIPF
  • Modelling and simulation: a computational perspective in anticancer drug discovery.
    Curr Med Chem Anticancer Agents, Vol. 4, No. 5. (September 2004), pp. 401-403.
    by F Gago
    posted to algorithms cancer docking drug ligand protein review by marcius on 2006-10-21 14:08:41 as ** along with 1 person and 4 groups sangeetha Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
  • Docking: successes and challenges.
    Curr Pharm Des, Vol. 11, No. 3. (2005), pp. 323-333.
    by V Mohan, AC Gibbs, MD Cummings, EP Jaeger, RL DesJarlais
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:08:05 as ** along with 1 person and 2 groups kazemi BioinfoCIPF SGU-CIPF
  • New methodologies for ligand-based virtual screening.
    Curr Pharm Des, Vol. 11, No. 9. (2005), pp. 1189-1202.
    by FL Stahura, J Bajorath
    posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:03:11 as ** along with 1 person and 4 groups sangeetha Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
  • A comparative docking study and the design of potentially selective MMP inhibitors.
    J Comput Aided Mol Des, Vol. 15, No. 10. (October 2001), pp. 873-881.
    by S Hanessian, N Moitessier, E Therrien
    posted to algorithms docking ligand protein by marcius on 2006-10-21 14:01:55 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • kinDOCK: a tool for comparative docking of protein kinase ligands.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by L Martin, V Catherinot, G Labesse
    posted to algorithms comparative_docking docking servers by marcius on 2006-10-21 14:00:50 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Evaluation of docking performance: comparative data on docking algorithms.
    J Med Chem, Vol. 47, No. 3. (29 January 2004), pp. 558-565.
    by M Kontoyianni, LM McClellan, GS Sokol
    posted to algorithms docking review by marcius on 2006-10-21 13:59:39 as ** along with 4 people and 5 groups yongzhao sangeetha insilico schuwi Bioinformatics TSRI_MGL insilicodrug BioinfoCIPF SGU-CIPF
  • The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
    Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119.
    by JS McCaskill
    posted to algorithms biophysics rna secondary_structure by marcius on 2006-10-20 14:24:37 as ** along with 5 people and 3 groups evaf arcticrasta condon Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
  • Bayesian search of functionally divergent protein subgroups and their function specific residues
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2466-2474.
    by Marttinen, Pekka, Corander, Jukka, Toronen, Petri, Holm, Liisa
    posted to algorithms bioinformatics protein_function by marcius on 2006-10-20 13:21:03 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Mining frequent stem patterns from unaligned RNA sequences
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2480-2487.
    by Hamada, Michiaki, Tsuda, Koji, Kudo, Taku, Kin, Taishin, Asai, Kiyoshi
    posted to algorithms alignment bioinformatics rna by marcius on 2006-10-20 13:20:33 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Computational methods for RNA structure determination.
    Curr Opin Struct Biol, Vol. 11, No. 3. (June 2001), pp. 282-286.
    by F Major, R Griffey
    posted to algorithms bioinformatics review rna structure by marcius on 2006-09-13 15:18:38 as ** along with 3 people and 2 groups lillekatt P2324548 eckart_bindewald BioinfoCIPF SGU-CIPF
  • How do RNA folding algorithms work?
    Nature Biotechnology, Vol. 22, No. 11., 1457.
    by Sean R Eddy
    posted to algorithms bioinformatics biophysics folding review rna by marcius on 2006-09-08 11:14:16 as ** along with 10 people and 2 groups evaf tardigrade mtagaya 3times3 cthachuk magnolia maralena guxiyou cambray austin BioinfoCIPF SGU-CIPF
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
    BMC Bioinformatics, Vol. 7 (04 September 2006), 400.
    by Robin D Dowell, Sean R Eddy
    posted to algorithms alignment bioinformatics prediction rna structure by marcius on 2006-09-07 22:04:11 as ** along with 4 people and 2 groups eckart_bindewald dquest ilh reyez BioinfoCIPF SGU-CIPF
  • Probabilistic annotation of protein sequences based on functional classifications.
    BMC Bioinformatics, Vol. 6 (2005)
    by ED Levy, CA Ouzounis, WR Gilks, B Audit
    posted to algorithms bioinformatics protein_function statistics by marcius on 2006-09-07 17:17:23 as ** along with 2 people and 2 groups sgoetz shung BioinfoCIPF SGU-CIPF
  • Computer modeling 16 S ribosomal RNA
    Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907.
    by John M Hubbard, John E Hearst
    posted to algorithms bioinformatics rna structure_prediction by marcius on 2006-09-07 13:31:07 as ** along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
  • Secondary Structure Prediction of Interacting RNA Molecules
    Journal of Molecular Biology, Vol. 345, No. 5., pp. 987-1001.
    by Mirela Andronescu, Zhi C Zhang, Anne Condon
    posted to algorithms bioinformatics rna secondary_structure software by marcius on 2006-09-06 10:36:45 as ** along with 4 people and 2 groups eckart_bindewald Hosna cthachuk physics BioinfoCIPF SGU-CIPF
  • A new algorithm for RNA secondary structure design.
    J Mol Biol, Vol. 336, No. 3. (20 February 2004), pp. 607-624.
    by M Andronescu, AP Fejes, F Hutter, HH Hoos, A Condon
    posted to algorithms bioinformatics rna secondary_structure software by marcius on 2006-09-06 10:36:07 as ** along with 5 people and 4 groups eckart_bindewald gane5h cthachuk mgaldzic smallbadguy 18th-century_history_culture_and_society BioinfoCIPF SGU-CIPF CHIP
  • Analysis of internal loops within the RNA secondary structure in almost quadratic time
    Bioinformatics, Vol. 22, No. 11. (1 June 2006), pp. 1317-1324.
    by Ogurtsov, Y Aleksey, Shabalina, A Svetlana, Kondrashov, S Alexey, Roytberg, A Mikhail
    posted to algorithms rna secondary_structure by marcius on 2006-09-06 10:35:26 as ** along with 1 person and 2 groups cthachuk BioinfoCIPF SGU-CIPF
  • Searching RNA motifs and their intermolecular contacts with constraint networks.
    Bioinformatics (4 July 2006)
    by P Thébault, S de Givry, T Schiex, C Gaspin
    posted to algorithms bioinformatics motif rna by marcius on 2006-08-23 13:32:31 as ** along with 3 people and 4 groups tardigrade dquest bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
  • CONTRAfold: RNA secondary structure prediction without physics-based models.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by CB Do, DA Woods, S Batzoglou
    posted to algorithms bioinformatics rna secondary_structure statistics by marcius on 2006-08-23 13:19:28 as ** along with 6 people and 3 groups balajis tardigrade penka condon acarbo austin beta BioinfoCIPF SGU-CIPF
  • An algorithm for detecting homologues of known structured RNAs in genomes.
    Proc IEEE Comput Syst Bioinform Conf (2004), pp. 300-310.
    by SY Le, JV Maizel, K Zhang
    posted to algorithms bioinformatics rna structure by marcius on 2006-07-13 10:23:58 as ** along with 2 people and 4 groups arcticrasta bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
  • Memory efficient folding algorithms for circular RNA secondary structures
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1172-1176.
    by Ivo L Hofacker, Peter F Stadler
    posted to algorithms bioinformatics folding programming rna secondary_structure by marcius on 2006-05-09 03:57:20 as ** along with 1 person and 2 groups ilh BioinfoCIPF SGU-CIPF
  • StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
    Bioinformatics, Vol. 22, No. 13. (1 July 2006), pp. 1593-1599.
    by Dalli, Deniz, Wilm, Andreas, Mainz, Indra, Steger, Gerhard
    posted to algorithms alignment bioinformatics rna by marcius on 2006-04-25 18:11:52 as ** along with 4 people and 4 groups eckart_bindewald ilh papamicd bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
  • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 195-201.
    by Konstantin Arnold, Lorenza Bordoli, Jurgen Kopp, Torsten Schwede
    posted to algorithms protein_structure servers structure_prediction by marcius on 2006-02-02 05:48:58 as ** along with 2 people and 2 groups chad_davis ffranca BioinfoCIPF SGU-CIPF
  • 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133.
    by Jean-Christophe Gelly, Alexandre G de Brevern, Serge Hazout
    posted to algorithms bioinformatics protein_fragments protein_structure by marcius on 2006-02-02 05:44:16 as ** along with 7 people and 4 groups MarcoAlvarez ana barry dimka ttjoseph nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement
    Protein Engineering, Design and Selection, Vol. 19, No. 2. (February 2006), pp. 55-65.
    by Wei Zhang, Yong Duan
    posted to ab-initio algorithms biophysics computational_biology protein_structure structure_prediction by marcius on 2006-01-27 01:13:40 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • RNAlign program: alignment of RNA sequences using both primary and secondary structures.
    Comput Appl Biosci, Vol. 10, No. 4. (July 1994), pp. 389-399.
    by F Corpet, B Michot
    posted to algorithms rna secondary_structure by marcius on 2005-12-21 19:29:25 as ** along with 1 person and 2 groups evaf BioinfoCIPF SGU-CIPF
  • Cofolga: a genetic algorithm for finding the common folding of two RNAs.
    Comput Biol Chem, Vol. 29, No. 2. (April 2005), pp. 111-119.
    by A Taneda
    posted to algorithms bioinformatics rna sequence_alignment by marcius on 2005-10-23 19:17:01 as ** along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
  • Predicting RNA structure using mutual information.
    Appl Bioinformatics, Vol. 4, No. 1. (2005), pp. 53-59.
    by E Freyhult, V Moulton, P Gardner
    posted to algorithms bioinformatics rna sequence_alignment by marcius on 2005-10-23 19:15:56 as ** along with 4 people and 2 groups evaf eckart_bindewald eweaver arcticrasta BioinfoCIPF SGU-CIPF
  • P-RnaPredict--a parallel evolutionary algorithm for RNA folding: effects of pseudorandom number quality.
    IEEE Trans Nanobioscience, Vol. 4, No. 3. (September 2005), pp. 219-227.
    by KC Wiese, A Hendriks, A Deschênes, B Ben Youssef
    posted to algorithms bioinformatics evolution rna by marcius on 2005-10-23 19:14:02 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • MicroRNA identification based on sequence and structure alignment.
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3610-3614.
    by X Wang, J Zhang, F Li, J Gu, T He, X Zhang, Y Li
    posted to algorithms bioinformatics rna sequence_alignment structure_alignment by marcius on 2005-10-23 03:17:36 as *** along with 2 people and 2 groups eckart_bindewald bioinfo BioinfoCIPF SGU-CIPF
  • ARTS: alignment of RNA tertiary structures.
    Bioinformatics, Vol. 21 Suppl 2 (1 September 2005)
    by O Dror, R Nussinov, H Wolfson
    posted to algorithms rna structure_alignment by marcius on 2005-10-23 03:11:36 as **** along with 2 groups BioinfoCIPF SGU-CIPF
  • Noncoding RNA gene detection using comparative sequence analysis.
    BMC Bioinformatics, Vol. 2, No. 1. (2001)
    by E Rivas, SR Eddy
    posted to algorithms bioinformatics rna by marcius on 2005-10-23 03:10:54 as *** along with 4 people and 2 groups evaf eckart_bindewald arcticrasta jarasch BioinfoCIPF SGU-CIPF
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