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タグ: bioinf_methods [65 articles]

Recent papers classified by the tag bioinf_methods.
  • Automatic Analysis of Protein Conformational Changes by Multiple Linkage Clustering
    Journal of Molecular Biology, Vol. 253, No. 4. (3 November 1995), pp. 633-647.
    by Nathalie S Boutonnet, Marianne J Rooman, Shoshana J Wodak
    posted to bioinf_methods protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-09-28 01:16:22 as ***** along with 1 group structural_bioinformatics
  • A simple physical model for binding energy hot spots in protein-protein complexes
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by Tanja Kortemme, David Baker
    posted to bioinf_methods gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 20:11:47 as ***** along with 1 group structural_bioinformatics
  • Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis.
    Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 164-178.
    by WR Atchley, KR Wollenberg, WM Fitch, W Terhalle, AW Dress
    posted to bioinf_methods protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-08-01 22:49:52 as **** along with 1 person and 1 group friendpine structural_bioinformatics
  • Application of torsion angle molecular dynamics for efficient sampling of protein conformations
    Journal Of Computational Chemistry, Vol. 26, No. 15. (30 November 2005), pp. 1565-1578.
    by Jianhan Chen, Wonpil Im, Charles L Brooks
    posted to bioinf_methods md_simulation torsion_angles by barry to the group Bioinformatics on 2005-10-03 19:29:19 as ** along with 1 group structural_bioinformatics
  • HCPM--program for hierarchical clustering of protein models.
    Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3179-3180.
    by D Gront, A Kolinski
    posted to bioinf_methods protein_structure structure_comparison by barry to the group Bioinformatics on 2006-03-06 22:17:59 as ** along with 2 people and 1 group dgront rabio structural_bioinformatics
  • Kinetics of protein-protein association explained by Brownian dynamics computer simulation.
    Proc Natl Acad Sci U S A, Vol. 89, No. 8. (15 April 1992), pp. 3338-3342.
    by SH Northrup, HP Erickson
    posted to bd_simulation bioinf_methods electrostatics by barry to the group Bioinformatics on 2005-10-11 23:23:18 as ** along with 1 group structural_bioinformatics
  • Protein-protein interactions: a review of protein dimer structures.
    Prog Biophys Mol Biol, Vol. 63, No. 1. (1995), pp. 31-65.
    by S Jones, JM Thornton
    posted to bioinf_methods protein_protein protein_structure review by barry to the group Bioinformatics on 2005-12-07 23:47:30 as *** along with 2 people and 4 groups chad_davis joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • A database of macromolecular motions
    Nucleic Acids Research, Vol. 26, No. 18. (15 September 1998), pp. 4280-4290.
    by M Gerstein, W Krebs
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-09-28 01:13:56 as read along with 1 group structural_bioinformatics
  • A tutorial of recent developments in the seeding of local alignment.
    J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 819-842.
    by DG Brown, M Li, B Ma
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group Bioinformatics on 2006-01-25 03:04:09 as * along with 1 person and 1 group nedwards structural_bioinformatics
  • Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
    Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 57-95.
    by Jeffry D Madura, James M Briggs, Rebecca C Wade, Malcolm E Davis, Brock A Luty, Andrew Ilin, Jan Antosiewicz, Michael K Gilson, Babak Bagheri, Ridgway L Scott, Andrew J Mccammon
    posted to bd_simulation bioinf_methods electrostatics by barry to the group Bioinformatics on 2005-10-11 02:25:41 as read along with 1 person and 1 group sim82 structural_bioinformatics
  • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2850-2855.
    by AS Aytuna, A Gursoy, O Keskin
    posted to bioinf_methods protein_protein protein_sequence protein_structure by barry to the group Bioinformatics on 2006-03-06 22:03:40 as ** along with 4 people and 1 group apaydin bicko j3xucite dyermd structural_bioinformatics
  • Electrotactins: a class of adhesion proteins with conserved electrostatic and structural motifs.
    Protein Eng, Vol. 11, No. 6. (June 1998), pp. 415-420.
    by SA Botti, CE Felder, JL Sussman, I Silman
    posted to bioinf_methods electrostatics protein_evolution protein_structure by barry to the group Bioinformatics on 2005-10-10 09:22:28 as *** along with 1 group structural_bioinformatics
  • Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.
    Proteins, Vol. 30, No. 2. (1 February 1998), pp. 144-154.
    by S Hayward, HJ Berendsen
    posted to bioinf_methods domain_motions protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-10-09 08:22:02 as read along with 1 group structural_bioinformatics
  • Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
    Protein Sci, Vol. 3, No. 5. (May 1994), pp. 769-778.
    by D Fischer, H Wolfson, SL Lin, R Nussinov
    posted to bioinf_methods protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-09-19 22:03:37 as ***** along with 4 people and 1 group aalibes shadowman tjimenez chrys structural_bioinformatics
  • Dynamite extended: two new services to simplify protein dynamic analysis
    Bioinformatics (Oxford, England), Vol. 21, No. 14. (15 July 2005), pp. 3174-3175.
    by Paul C Barrett, Martin E Noble
    posted to bioinf_methods pca by barry to the group Bioinformatics on 2005-10-03 19:22:26 as ** along with 1 group structural_bioinformatics
  • Insights into Protein-Protein Interfaces using a Bayesian Network Prediction Method
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by James R Bradford, Chris J Needham, Andrew J Bulpitt, David R Westhead
    posted to bayesian_classifiers bioinf_methods protein_protein by barry to the group Bioinformatics on 2006-08-28 18:00:47 as ** along with 7 people and 1 group conkymacro ameetsoni grahamc massivemayhem phoenixzxl marti paolomarcatili structural_bioinformatics
  • Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter
    Methods, Vol. 14, No. 3. (March 1998), pp. 329-341.
    by Razif R Gabdoulline, Rebecca C Wade
    posted to bd_simulation bioinf_methods electrostatics by barry to the group Bioinformatics on 2005-10-11 03:54:33 as ***** along with 1 person and 1 group Martin8223 structural_bioinformatics
  • An information-theoretic definition of similarity
    (1998), pp. 296-304.
    by Dekang Lin
    posted to bioinf_methods protein_sequence similarity by barry to the group Bioinformatics on 2005-04-26 08:03:05 as * along with 23 people and 15 groups camster dbk sourada korakot LeightonP frednicolier parmentierf JacquesC mortimer mote lwilliams jelsas jtextori ingo gangli garyfeng okarsligil onlyme gaudan macavity1g Tronhus CitoJam sgoetz streptomyces NU-PRL Philosophy_of_Information UoY-CS-AIG dbk-lab Blog_and_Wiki_Research structural_bioinformatics tulip ReadingLab ASR ISI NLP SLA LanguageAndBrain AI
  • Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN.
    J Mol Biol, Vol. 196, No. 3. (5 August 1987), pp. 611-639.
    by G Wagner, W Braun, TF Havel, T Schaumann, N Go, K Wüthrich
    posted to bioinf_methods distance_matrices nmr by barry to the group Bioinformatics on 2006-02-24 00:07:00 as ** along with 1 group structural_bioinformatics
  • PISCES: a protein sequence culling server.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1589-1591.
    by G Wang, RL Dunbrack
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-19 21:59:58 as ** along with 8 people and 1 group aalibes kaarsinogen j3xucite dgront blackbart mloewer ezralanglois chgjb structural_bioinformatics
  • Travel depth, a new shape descriptor for macromolecules: application to ligand binding.
    J Mol Biol, Vol. 362, No. 3. (22 September 2006), pp. 441-458.
    by RG Coleman, KA Sharp
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-01-30 20:08:02 as ** along with 1 person and 1 group nickolay structural_bioinformatics
  • Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 673-692.
    by AF Neuwald, N Kannan, A Poleksic, N Hata, JS Liu
    posted to allosteric bioinf_methods contacts core_residues g_proteins ntpases p-loop protein_design protein_dynamics protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2006-01-07 03:57:13 as ***** along with 1 group structural_bioinformatics
  • A method to predict functional residues in proteins.
    Nat Struct Biol, Vol. 2, No. 2. (February 1995), pp. 171-178.
    by G Casari, C Sander, A Valencia
    posted to bioinf_methods correlated_mutations protein_design protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-16 23:37:03 as read along with 1 person and 1 group sriram_s structural_bioinformatics
  • Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin.
    J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 149-162.
    by AH Elcock, RR Gabdoulline, RC Wade, JA McCammon
    posted to bd_simulation bioinf_methods electrostatics by barry to the group Bioinformatics on 2005-10-11 02:13:35 as *** along with 2 people and 1 group mikaellund Martin8223 structural_bioinformatics
  • Multivariate Analysis of Conserved Sequence-Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain
    Journal of Molecular Biology, Vol. 368, No. 5. (18 May 2007), pp. 1231-1248.
    by Barry J Grant, Andrew J Mccammon, Leo S Caves, Robert A Cross
    posted to torsion_angles swi-swii structural_bioinformatics sca r protein_structure protein_sequence protein_dynamics pca p-loop ntpases molecular_motors mine kinesin domain_motions correlated_motions core_structure clustering bioinf_methods by barry to the group Bioinformatics on 2007-04-27 17:41:06 as read along with 3 people and 1 group choonpeng cactus insectopalo structural_bioinformatics
  • Coarse-grained normal mode analysis in structural biology
    Current Opinion in Structural Biology, Vol. 15, No. 5. (October 2005), pp. 586-592.
    by Ivet Bahar, Aj Rader
    posted to bioinf_methods nma review by barry to the group Bioinformatics on 2005-10-03 19:18:42 as ** along with 7 people and 1 group BragilMassoud apaydin aqeel shuns scis0000001 insectopalo higueruelo structural_bioinformatics
  • Residue depth: a novel parameter for the analysis of protein structure and stability.
    Structure, Vol. 7, No. 7. (15 July 1999), pp. 723-732.
    by S Chakravarty, R Varadarajan
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-02-06 19:34:03 as ** along with 1 group structural_bioinformatics
  • Linked: How Everything Is Connected to Everything Else and What It Means for Business, Science, and Everyday Life
    (01 April 2003)
    by Albert-Laszlo Barabasi
    posted to bioinf_methods networks small_world by barry to the group Bioinformatics on 2005-04-26 08:04:18 as **** along with 65 people and 32 groups camster draggin korakot Mandre A_Olympia zephoria RyanSchultz fmatthes scholz cyprien riadlem lehel Rsavi zinp nkorf tautai wcrosbie cchesher cmmorel jekky Typewriter mbliemel Jenneke cgjj slariccia irinas petzlux marije seawidget hannont matteodellamico leonardo bibliothecaire bigbossman krisl spirit_of_numenor cristinaalp brusilovsky jwdietrich britton cerkut awooga mzygmunt azygmunt RafG jaspervoskuilen OriginalLurch timflutre alexevasion flavian_vasile mattlandau PaulBHartzog roland_ewald jenna anansi sidds1601 rkalvi JimFolk asrilova anton-tayanovskyy aelzaim copyculture kamccollum kikimu thecolourblue CMU-HCII Philosophy_of_Information dbk-lab Blog_and_Wiki_Research automatic_summarization structural_bioinformatics CSCW MathBio ASR digital_youth Sociology Librarians Semantic-Social-Networks Wikipedia CoP_CMS folksonomy ETEC533 CMS Cybernetics social_navigation ComplexAdaptiveSystems Biomedical_Cybernetics AGH-IISG Adaptive-Web dIEMoSIRIS MoSi-Rostock AQUA-FONTIS-Study MASSS CSU_School_of_Education Web2-0_Education Social Web ICT4D
  • In silico Discovery of Enzyme-Substrate Specificity-determining Residue Clusters
    Journal of Molecular Biology, Vol. 352, No. 5. (7 October 2005), pp. 1105-1117.
    by Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Rajesh Munavalli, Al Geist, Nagiza F Samatova
    posted to bioinf_methods correlated_mutations protein_design protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-15 18:06:44 as **** along with 1 person and 1 group cjeans structural_bioinformatics
  • Domain identification by iterative analysis of error-scaled difference distance matrices
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2269-2275.
    by Schneider,
    posted to bioinf_methods core_structure distance_matrices domain_motions by barry to the group Bioinformatics on 2006-02-23 02:01:05 as ** along with 1 group structural_bioinformatics
  • Constrained geometric simulation of diffusive motion in proteins
    Physical Biology, Vol. 2, No. 4. (December 2005), S127.
    by Stephen Wells, Scott Menor, Brandon Hespenheide, MF Thorpe
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-01-09 18:36:48 as ** along with 2 people and 1 group apaydin higueruelo structural_bioinformatics
  • Soft protein-protein docking in internal coordinates.
    Protein Sci, Vol. 11, No. 2. (February 2002), pp. 280-291.
    by J Fernández-Recio, M Totrov, R Abagyan
    posted to bioinf_methods protein_protein by barry to the group Bioinformatics on 2005-10-17 18:49:54 as ** along with 5 people and 1 group bicko bluvsh1 cjeans selrac wilbur structural_bioinformatics
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to bioinf_methods protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-17 18:52:59 as ** along with 3 people and 1 group jwm bicko bluvsh1 structural_bioinformatics
  • Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics.
    Protein Eng, Vol. 14, No. 4. (April 2001), pp. 209-217.
    by AC May
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group Bioinformatics on 2006-05-04 17:16:42 as **** along with 1 group structural_bioinformatics
  • Computational alanine scanning of protein-protein interfaces.
    Sci STKE, Vol. 2004, No. 219. (10 February 2004)
    by T Kortemme, DE Kim, D Baker
    posted to bioinf_methods protein_protein protein_structure by barry to the group Bioinformatics on 2005-12-07 23:56:00 as ***** along with 4 people and 5 groups sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f.
    Biophys J, Vol. 81, No. 6. (December 2001), pp. 3090-3104.
    by F De Rienzo, RR Gabdoulline, MC Menziani, PG De Benedetti, RC Wade
    posted to bd_simulation bioinf_methods electrostatics by barry to the group Bioinformatics on 2005-10-11 02:09:35 as ** along with 1 group structural_bioinformatics
  • Fast embedding methods for clustering tens of thousands of sequences.
    Computational biology and chemistry, Vol. 32, No. 4. (August 2008), pp. 282-286.
    by G Blackshields, M Larkin, IM Wallace, A Wilm, DG Higgins
    posted to bioinf_methods clustering protein_sequence by barry to the group Bioinformatics on 2008-08-23 20:27:35 as **** along with 1 group structural_bioinformatics
  • New tools and data for improving structures, using all-atom contacts.
    Methods Enzymol, Vol. 374 (2003), pp. 385-412.
    by JS Richardson, WA Bryan, DC Richardson
    posted to bioinf_methods contacts protein_structure by barry to the group Bioinformatics on 2005-09-28 00:56:39 as ***** along with 1 person and 4 groups joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1365-1373.
    by BJ McConkey, V Sobolev, M Edelman
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-02-06 19:32:08 as ** along with 3 people and 1 group bicko j3xucite siebertm structural_bioinformatics
  • Very fast empirical prediction and rationalization of protein pKa values.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 704-721.
    by H Li, AD Robertson, JH Jensen
    posted to bioinf_methods md_simulation pka by barry to the group Bioinformatics on 2008-04-25 20:55:37 as ** along with 4 people bicko sim82 sunhwan mschofie
  • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2256-2268.
    by Krissinel, , Henrick,
    posted to structure_comparison protein_structure graph bioinf_methods by barry to the group Bioinformatics on 2007-07-13 19:39:15 as read along with 3 people and 3 groups jwm analogAI robert structural_bioinformatics Radiation_Damage Stressosome
  • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
    Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62.
    by JH Lin, AL Perryman, JR Schames, JA McCammon
    posted to bioinf_methods docking drug_design md_simulation protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-09-07 20:06:11 as ** along with 4 people and 2 groups blackbart kazemi sobolevnrm LamBras structural_bioinformatics baker-group
  • Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.
    Proc Natl Acad Sci U S A, Vol. 97, No. 7. (28 March 2000), pp. 3288-3291.
    by KR Wollenberg, WR Atchley
    posted to bioinf_methods protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-08-01 22:45:50 as *** along with 1 person and 1 group friendpine structural_bioinformatics
  • notes Tracing evolutionary pressure
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 908-915.
    by Kai Ye, Gert Vriend, Adriaan P Ijzerman
    posted to bioinf_methods phylogeny protein_evolution protein_sequence residue_annotation by barry to the group Bioinformatics on 2008-04-11 19:13:22 as *** along with 2 people and 1 group sunhwan gulkur structural_bioinformatics
  • Identifying DNA-binding proteins using structural motifs and the electrostatic potential
    Nucleic Acids Research, Vol. 32, No. 16. (2004), pp. 4732-4741.
    by Hugh P Shanahan, Mario A Garcia, Susan Jones, Janet M Thornton
    posted to bioinf_methods protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:42:27 as ** along with 1 group structural_bioinformatics
  • Statistical analysis and prediction of protein-protein interfaces
    Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3. (19 May 2005), pp. 353-366.
    by Andrew J Bordner, Ruben Abagyan
    posted to bioinf_methods protein_protein svm by barry to the group Bioinformatics on 2005-10-17 18:44:16 as ** along with 6 people and 1 group bicko lyongu ameetsoni cjeans Evangelia marti structural_bioinformatics
  • Protein flexibility using constraints from molecular dynamics simulations
    Physical Biology, Vol. 2, No. 4. (December 2005), S137.
    by Tatyana Mamonova, Brandon Hespenheide, Rachel Straub, MF Thorpe, Maria Kurnikova
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-01-09 18:30:27 as ** along with 1 person and 2 groups Poincare structural_bioinformatics Algorithms
  • A comprehensive and non-redundant database of protein domain movements.
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2832-2838.
    by G Qi, R Lee, S Hayward
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-09-28 01:41:03 as **** along with 1 group structural_bioinformatics
  • Predicting conformational switches in proteins
    Protein Science, Vol. 8, No. 9. (1999), pp. 1752-1764.
    by M Young, K Kirshenbaum, KA Dill, S Highsmith
    posted to bioinf_methods protein_dynamics protein_sequence by barry to the group Bioinformatics on 2005-09-28 01:06:18 as * along with 1 group structural_bioinformatics
  • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (2006), pp. 347-361.
    by Kim Sharp, John J Skinner
    posted to protein_structure protein_dynamics md_simulation bioinf_methods allosteric by barry to the group Bioinformatics on 2007-01-30 20:09:59 as **** along with 3 people and 2 groups lna choonpeng sobolevnrm structural_bioinformatics baker-group
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