marcius's algorithms [56 articles] Export

Recent papers added to marcius's library classified by the tag 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. [My Copy] 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. [My Copy] 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 9 people and 3 groups martainn calderonv wiedenhoeft jameswasmuth icases tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
	An RNA folding algorithm including pseudoknots based on dynamic weighted matching. [My Copy] 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 [My Copy] 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. [My Copy] 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 [My Copy] 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 [My Copy] 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 [My Copy] PLoS Comput Biol, Vol. 2, No. 7. (21 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 8 people and 2 groups karthikraman chica RebeccaHamer robfsouza jeremymiller chad_davis skhadar dquest BioinfoCIPF SGU-CIPF
	Structural Modeling of Protein Interactions by Analogy: Application to PSD-95 [My Copy] PLoS Computational Biology, Vol. preprint, No. 2006. (1 October 2006) by Dmitry Korkin, Fred P. Davis, Frank Alber, et al.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 2 groups BioinfoCIPF SGU-CIPF
	The many faces of protein-protein interactions: A compendium of interface geometry. [My Copy] PLoS computational biology, Vol. 2, No. 9. (29 September 2006), e124. by Wan Kyu 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 10 people and 2 groups winterschlaefer zdai raik bicko chad_davis choonpeng Evangelia wilbur allmensch marck BioinfoCIPF SGU-CIPF
	Evaluation of library ranking efficacy in virtual screening. [My Copy] J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 11-22. by M. Kontoyianni, G. S. Sokol, L. M. 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. [My Copy] Mini Rev Med Chem, Vol. 4, No. 7. (September 2004), pp. 779-791. by X. Barril, R. E. Hubbard, S. D. 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. [My Copy] Curr Opin Drug Discov Devel, Vol. 7, No. 4. (July 2004), pp. 396-403. by A. N. 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. [My Copy] Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949. by D. B. Kitchen, H. Decornez, J. R. Furr, J. Bajorath posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:16:46 as along with 8 people and 9 groups LamBras robert85 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. [My Copy] Med Chem, Vol. 2, No. 1. (January 2006), pp. 89-112. by M. J. 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. [My Copy] 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. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted to algorithms docking drug ligand protein review by marcius on 2006-10-21 14:11:15 as along with 6 people and 5 groups klexa csrocha oteri sangeetha schlauchi massivemayhem Structural Biology Group TorVergata Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Computational tools for protein modeling. [My Copy] Current protein & peptide science, Vol. 1, No. 1. (July 2000), pp. 1-21. by D. Xu, Y. Xu, E. C. Uberbacher posted to algorithms protein review by marcius on 2006-10-21 14:10:31 as along with 3 people and 2 groups wilbur flbarroso granujilla BioinfoCIPF SGU-CIPF
	Modelling and simulation: a computational perspective in anticancer drug discovery. [My Copy] 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. [My Copy] Curr Pharm Des, Vol. 11, No. 3. (2005), pp. 323-333. by V. Mohan, A. C. Gibbs, M. D. Cummings, E. P. Jaeger, R. L. 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. [My Copy] Curr Pharm Des, Vol. 11, No. 9. (2005), pp. 1189-1202. by F. L. 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. [My Copy] 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. [My Copy] 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. [My Copy] J Med Chem, Vol. 47, No. 3. (29 January 2004), pp. 558-565. by M. Kontoyianni, L. M. McClellan, G. S. Sokol posted to algorithms docking review by marcius on 2006-10-21 13:59:39 as along with 5 people and 5 groups oteri yongzhao sangeetha insilico schuwi Bioinformatics TSRI_MGL insilicodrug BioinfoCIPF SGU-CIPF
	The equilibrium partition function and base pair binding probabilities for RNA secondary structure. [My Copy] Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119. by J. S. McCaskill posted to algorithms biophysics rna secondary_structure by marcius on 2006-10-20 14:24:37 as along with 9 people and 3 groups NicholasErho saunders rb_india ellarond evaf arcticrasta condon Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
	Bayesian search of functionally divergent protein subgroups and their function specific residues [My Copy] Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2466-2474. by Marttinen, Pekka, Corander, et al. 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 [My Copy] Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2480-2487. by Hamada, Michiaki, Tsuda, et al. 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. [My Copy] 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? [My Copy] Nature biotechnology, Vol. 22, No. 11. (November 2004), pp. 1457-1458. by S. R. Eddy posted to algorithms bioinformatics biophysics folding review rna by marcius on 2006-09-08 11:14:16 as along with 14 people and 2 groups guhjy heliopais mjoach ellarond evaf tardigrade mtagaya 3times3 cthachuk magnolia maralena guxiyou cambray austin BioinfoCIPF SGU-CIPF
	Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (04 September 2006), 400. by Robin Dowell, Sean Eddy posted to algorithms alignment bioinformatics prediction rna structure by marcius on 2006-09-07 22:04:11 as along with 6 people and 2 groups nuin rb_india eckart_bindewald dquest ilh reyez BioinfoCIPF SGU-CIPF
	Probabilistic annotation of protein sequences based on functional classifications. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by E. D. Levy, C. A. Ouzounis, W. R. 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 [My Copy] 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 [My Copy] 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 5 people and 2 groups rb_india eckart_bindewald Hosna cthachuk physics BioinfoCIPF SGU-CIPF
	A new algorithm for RNA secondary structure design. [My Copy] J Mol Biol, Vol. 336, No. 3. (20 February 2004), pp. 607-624. by M. Andronescu, A. P. Fejes, F. Hutter, H. H. Hoos, A. Condon posted to algorithms bioinformatics rna secondary_structure software by marcius on 2006-09-06 10:36:07 as along with 6 people and 4 groups gzm55 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. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 11. (1 June 2006), pp. 1317-1324. by A. Y. Ogurtsov, S. A. Shabalina, A. S. Kondrashov, M. A. Roytberg posted to algorithms rna secondary_structure by marcius on 2006-09-06 10:35:26 as along with 2 people and 2 groups hendrik85 cthachuk BioinfoCIPF SGU-CIPF
	Searching RNA motifs and their intermolecular contacts with constraint networks. [My Copy] 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. [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006) by C. B. Do, D. A. Woods, S. Batzoglou posted to algorithms bioinformatics rna secondary_structure statistics by marcius on 2006-08-23 13:19:28 as along with 7 people and 3 groups gulkur balajis tardigrade penka condon acarbo austin beta BioinfoCIPF SGU-CIPF
	An algorithm for detecting homologues of known structured RNAs in genomes. [My Copy] Proc IEEE Comput Syst Bioinform Conf (2004), pp. 300-310. by S. Y. Le, J. V. 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 [My Copy] 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 [My Copy] Bioinformatics, Vol. 22, No. 13. (1 July 2006), pp. 1593-1599. by Dalli, Deniz, Wilm, et al. 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. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 2. (15 January 2006), pp. 195-201. by K. Arnold, L. Bordoli, J. Kopp, T. Schwede posted to algorithms protein_structure servers structure_prediction by marcius on 2006-02-02 05:48:58 as along with 5 people and 2 groups krapnik flbarroso hervelequere chad_davis ffranca BioinfoCIPF SGU-CIPF
	'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments [My Copy] 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 6 people and 4 groups 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 [My Copy] 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. [My Copy] 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. [My Copy] 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. [My Copy] 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. [My Copy] IEEE Trans Nanobioscience, Vol. 4, No. 3. (September 2005), pp. 219-227. by K. C. 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. [My Copy] Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3610-3614. by X. Wang, J. Zhang, F. Li, et al.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. [My Copy] 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 [My Copy] BMC Bioinformatics, Vol. 2, No. 1. (2001), 8. by Elena Rivas, Sean Eddy posted to algorithms bioinformatics rna by marcius on 2005-10-23 03:10:54 as along with 8 people and 2 groups stharward NicholasErho balaji myrtilus evaf eckart_bindewald arcticrasta jarasch BioinfoCIPF SGU-CIPF

Note: You may cite this page as: http://www.citeulike.org/user/marcius/tag/algorithms

Result page: 1 2 Next

rna	213
bioinformatics	196
review	127
biophysics	90
protein_structure	86
structure	86
evolution	86
structure_prediction	64
algorithms	56
computational_biology	53
secondary_structure	53
protein	43
folding	41
classification	38
ncrna	35
casp	35
drug	32
docking	32
protein_interactions	31
genome	30
function	29
microrna	27
cafasp	26
sequence_alignment	25
protein_function	24
software	23
views	22
servers	22
comparative_modeling	19
model_assessment	19
statistical_potentials	19
biology	18
structural_genomics	18
databases	17
ribosome	16
nmr	16
disease	16
protein_domains	15
ligand	15
protein_folding	15
bioengineering	14
clustering	14
protein_fragments	14
ab-initio	12
structure_alignment	11
genes	11
prediction	11
dna	10
statistics	9
snp	9
alignment	9
model_evaluation	8
membrane_protein	7
experimental	7
gene_expression	6
systems_biology	6
microarray	6
phylogeny	6
virus	5
mechano_receptors	5
foce_field	5
sequence	5
protein_threading	5
motif	5
molecular_dynamics	5
text_mining	4
ribozyme	4
discovery	4
rotamers	4
sequence-structure	4
protein_complexes	3
cancer	3
comparative_docking	3
server	3
news	3
human	3
interaction	3
meeting	3
immunology	2
programming	2
hypotesis	2
allosteric	2
proteomics	2
editorial	2
pleiotropy	2
pdb	2
hts	2
trypsin	1
ontology	1
loop_modeling	1
proteases	1
metabolomics	1
opensourcebiology	1
nucleosome	1
side_chains	1
protein_disorder	1
protein_design	1
nanotechnology	1
membrane	1
stability	1
disulfide	1
position	1
web20	1
malaria	1
congress	1
synthetic_biology	1
fold	1
glyco	1
dynamics	1
machine_learning	1
mysql	1
aminoacid_alphabets	1
metagenomics	1
php	1
molecular_mimicry	1
stem_cells	1
consensus	1
plant	1

marcius's algorithms [56 articles] Export

marcius's tags