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vavi's library [100 articles]

Recent papers added to vavi's library.
  • The anatomy of a large-scale hypertextual Web search engine
    Computer Networks and ISDN Systems, Vol. 30, No. 1--7. (1998), pp. 107-117.
    by Sergey Brin, Lawrence Page
    posted to engine google search by vavi on 2007-07-25 11:29:46 as read along with 59 people and 10 groups huitseeker abellogin RafG dmeister pprett rabourn lior Icequeen ansobol masaka jcaddy toomash ldfu macartisan indratmo rozim zelacerda xxc akrowne derinb michael_zimmer ChaTo schaal fsilvestri jarrodz manastungare MaineC seabay wcohen tolosoft lighttree ddahlem acharlier umurthy donade gane5h merazzle twetering BenediktM sudhanshu_goswami petzel mzygmunt kazama Repton abonchen PaulBHartzog candan rejin tonypia julia-krysztofiak Nicolas_Torzec saikrishna ttdevelop mdrosou jgronski clickstone votis federicopaoloni drakkos69 Blog_and_Wiki_Research CSCW InformationRetrieval Wikipedia OpenArchive P2P XMLDataManagement VTCS_PIM2006_Annotation VT_DLRL WebMining
  • Progress in Modeling of Protein Structures and Interactions
    Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642.
    by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker
    posted to protein review structure_prediction by vavi on 2006-11-29 14:59:03 as ** along with 13 people and 3 groups barry thaliana jwm bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain
    Protein Sci, Vol. 13, No. 3. (1 March 2004), pp. 608-616.
    by Christian Blouin, Davin Butt, Andrew J Roger
    posted to no-tag by vavi on 2006-10-11 18:04:25 as **
  • High-throughput computational and experimental techniques in structural genomics.
    Genome Res, Vol. 14, No. 10B. (October 2004), pp. 2145-2154.
    by MR Chance, A Fiser, A Sali, U Pieper, N Eswar, G Xu, JE Fajardo, T Radhakannan, N Marinkovic
    posted to no-tag by vavi on 2006-10-11 16:58:12 as ** along with 1 person dgront
  • Evolution and physics in comparative protein structure modeling.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 413-421.
    by A Fiser, M Feig, CL Brooks, A Sali
    posted to comparative_modeling structure_prediction by vavi on 2006-10-11 16:51:26 as ** along with 2 people and 2 groups barry insectopalo structural_bioinformatics Bioinformatics
  • An introduction to ROC analysis
    Pattern Recognition Letters, Vol. 27, No. 8. (June 2006), pp. 861-874.
    by Tom Fawcett
    posted to machine_learning by vavi on 2006-10-02 20:56:57 as ** along with 22 people and 6 groups nherveg jyuh isimpson AbnerCYH ldietz dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos cdeane haiyeong Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
  • Geometry-based flexible and symmetric protein docking.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 224-231.
    by D Schneidman-Duhovny, Y Inbar, R Nussinov, HJ Wolfson
    posted to docking flexdock protein by vavi on 2006-09-13 09:06:46 as ** along with 2 people and 2 groups bicko marcius BioinfoCIPF SGU-CIPF
  • Long loop prediction using the protein local optimization program.
    Proteins (22 August 2006)
    by Kai Zhu, David L L Pincus, Suwen Zhao, Richard A A Friesner
    posted to ab_initio loop_prediction protein by vavi on 2006-08-28 09:32:33 as *** along with 1 person cdeane
  • Approximate protein structural alignment in polynomial time.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12201-12206.
    by R Kolodny, N Linial
    posted to protein structure_alignment by vavi on 2006-08-15 14:57:20 as ** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • Predicting interresidue contacts using templates and pathways
    Proteins: Structure, Function, and Genetics, Vol. 53, No. S6. (2003), pp. 497-502.
    by Yu Shao, Christopher Bystroff
    posted to contact_map contact_map_prediction protein by vavi on 2006-08-15 14:20:02 as **
  • notes A contact map matching approach to protein structure similarity analysis.
    Genet Mol Res, Vol. 5, No. 2. (2006), pp. 284-308.
    by RC de Melo, CE Lopes, FA Fernandes, CH da Silveira, MM Santoro, RL Carceroni, W Meira, Ade A Araújo
    posted to contact_map image_processing protein_similarity by vavi on 2006-08-14 15:10:44 as ** along with 2 people dgront mijam
  • Geometric algorithms for the conformational analysis of long protein loops
    Journal of Computational Chemistry, Vol. 25, No. 7. (2004), pp. 956-967.
    by J Cortés, T Siméon, M Remaud-Siméon, V Tran
    posted to loop_analysis protein by vavi on 2006-08-14 11:00:43 as * along with 1 person aqeel
  • notes A combined optimization method for solving the inverse kinematics problems of mechanical manipulators
    Robotics and Automation, IEEE Transactions on, Vol. 7, No. 4. (1991), pp. 489-499.
    by LCT Wang, CC Chen
    posted to inverse_kinematics robotics by vavi on 2006-08-14 10:34:46 as ** along with 1 person and 1 group jimesh Inverse_Kinematics
  • LGA: A method for finding 3D similarities in protein structures.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3370-3374.
    by A Zemla
    posted to contact_map protein structure_comparison by vavi on 2006-08-13 14:28:27 as ** along with 3 people and 2 groups karbak ana analogAI structural_bioinformatics Bioinformatics
  • Model for haptoglobin heavy chain based upon structural homology.
    Proc Natl Acad Sci U S A, Vol. 77, No. 6. (June 1980), pp. 3393-3397.
    by J Greer
    posted to knowledge_based loop_modeling protein by vavi on 2006-08-06 13:21:44 as **
  • Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures.
    Pac Symp Biocomput (1996), pp. 570-589.
    by SD Rufino, LE Donate, L Canard, TL Blundell
    posted to classification loop_modeling protein by vavi on 2006-08-06 09:11:06 as ** along with 2 people Alan medic0747
  • ArchDB: automated protein loop classification as a tool for structural genomics.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by J Espadaler, N Fernandez-Fuentes, A Hermoso, E Querol, FX Aviles, MJ Sternberg, B Oliva
    posted to classification loop protein by vavi on 2006-08-06 09:06:23 as ** along with 1 person baldo
  • CODA: a combined algorithm for predicting the structurally variable regions of protein models.
    Protein Sci, Vol. 10, No. 3. (March 2001), pp. 599-612.
    by CM Deane, TL Blundell
    posted to hybrid protein structure_prediction by vavi on 2006-08-05 13:07:33 as ** along with 2 people medic0747 cdeane
  • notes Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 209-225.
    by KT Simons, C Kooperberg, E Huang, D Baker
    posted to comparative_modeling protein strutcture_prediction by vavi on 2006-07-31 13:48:24 as ** along with 7 people and 2 groups joule ana jwm wouterboomsma j3xucite hmk mijam structural_bioinformatics Bioinformatics
  • A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.
    Proteins, Vol. 40, No. 1. (1 July 2000), pp. 135-144.
    by CM Deane, TL Blundell
    posted to loop_modeling protein by vavi on 2006-07-31 12:27:08 as ** along with 3 people thamelry medic0747 cdeane
  • A divide and conquer approach to fast loop modeling
    Protein Eng., Vol. 15, No. 4. (1 April 2002), pp. 279-286.
    by Silvio C Tosatto, Eckart Bindewald, Jurgen Hesser, Reinhard Manner
    posted to ab_initio loop_modeling protein by vavi on 2006-07-31 10:31:02 as **
  • Cyclic coordinate descent: A robotics algorithm for protein loop closure.
    Protein Sci, Vol. 12, No. 5. (May 2003), pp. 963-972.
    by AA Canutescu, RL Dunbrack
    posted to kinematics loop_modeling protein by vavi on 2006-07-31 10:26:25 as ** along with 4 people and 1 group yongzhao j3xucite dgront mijam TSRI_MGL
  • Prediction of loop geometries using a generalized born model of solvation effects
    Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 173-183.
    by Chaya S Rapp, Richard A Friesner
    posted to ab_initio molecular_dynamics monte_carlo protein structure_prediction by vavi on 2006-07-31 09:23:54 as **
  • Conformational sampling using high-temperature molecular dynamics.
    Biopolymers, Vol. 29, No. 14. (December 1990), pp. 1847-1862.
    by RE Bruccoleri, M Karplus
    posted to loop_prediction molecular_dynamics protein by vavi on 2006-07-31 09:16:32 as **
  • Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
    Proteins, Vol. 46, No. 1. (1 January 2002), pp. 128-146.
    by Y Liu, DL Beveridge
    posted to ab_initio molecular_dynamics monte_carlo protein simulated_annealing structure_prediction by vavi on 2006-07-31 09:00:25 as **
  • Structural prediction of peptides bound to MHC class I.
    J Mol Biol, Vol. 356, No. 2. (17 February 2006), pp. 521-546.
    by T Fagerberg, JC Cerottini, O Michielin
    posted to molecular_dynamics protein simulated_annealing structure_prediction by vavi on 2006-07-31 08:54:09 as **
  • Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins
    Biopolymers, Vol. 32, No. 1. (1992), pp. 33-43.
    by Junichi Higo, Vincent Collura, Jean Garnier
    posted to loop_prediction simulated_annealing by vavi on 2006-07-30 14:22:44 as **
  • The loop problem in proteins: A monte carlo simulated annealing approach
    Biopolymers, Vol. 33, No. 8. (1993), pp. 1271-1286.
    by Louis Carlacci, Walter S Englander
    posted to loop_prediction monte_carlo protein simulated_annealing by vavi on 2006-07-30 14:18:24 as **
  • ModLoop: automated modeling of loops in protein structures.
    Bioinformatics, Vol. 19, No. 18. (12 December 2003), pp. 2500-2501.
    by A Fiser, A Sali
    posted to loop_prediction protein server by vavi on 2006-07-30 13:17:51 as ** along with 1 person tji
  • Protein modeling and structure prediction with a reduced representation.
    Acta Biochim Pol, Vol. 51, No. 2. (2004), pp. 349-371.
    by A Kolinski
    posted to protein strutcture_prediction by vavi on 2006-07-30 09:40:22 as ** along with 5 people mcbla mijam dgront rabio sekmi
  • Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.
    BMC Bioinformatics, Vol. 6 (28 June 2005)
    by W Boomsma, T Hamelryck
    posted to loop_modeling protein by vavi on 2006-07-25 16:52:24 as ** along with 3 people pansapiens wouterboomsma Alan
  • Ab initio protein structure prediction: progress and prospects.
    Annu Rev Biophys Biomol Struct, Vol. 30 (2001), pp. 173-189.
    by R Bonneau, D Baker
    posted to ab_initio protein review structure_prediction by vavi on 2006-07-25 14:29:29 as ** along with 1 person dgront
  • Tools for comparative protein structure modeling and analysis.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3375-3380.
    by N Eswar, B John, N Mirkovic, A Fiser, VA Ilyin, U Pieper, AC Stuart, MA Marti-Renom, MS Madhusudhan, B Yerkovich, A Sali
    posted to comparative_modeling protein strutcture_prediction by vavi on 2006-07-25 14:23:56 as ** along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
  • Comparative protein modelling by satisfaction of spatial restraints.
    J Mol Biol, Vol. 234, No. 3. (5 December 1993), pp. 779-815.
    by A Sali, TL Blundell
    posted to protein structure_prediction by vavi on 2006-07-25 13:44:57 as ** along with 11 people granujilla dimka bicko chad_davis ttjoseph skhadar dgront rabio massivemayhem medic0747 sebk
  • notes Saturating representation of loop conformational fragments in structure databanks
    BMC Structural Biology, Vol. 6 (04 July 2006), 15.
    by Narcis Fernandez-Fuentes, Andras Fiser
    posted to database fragments protein by vavi on 2006-07-25 11:21:49 as ** along with 3 people saunders iakes cdeane
  • A composite score for predicting errors in protein structure models.
    Protein Sci, Vol. 15, No. 7. (July 2006), pp. 1653-1666.
    by D Eramian, MY Shen, D Devos, F Melo, A Sali, MA Marti-Renom
    posted to protein_structure svm by vavi on 2006-07-25 10:39:39 as ** along with 4 people j3xucite dimka wouterboomsma mijam
  • notes Docking protein domains in contact space
    BMC Bioinformatics, Vol. 7, No. 1. (21 June 2006), 310.
    by Stefano Lise, Alice Walker-Taylor, David T Jones
    posted to contact_maps_use docking by vavi on 2006-07-25 10:21:34 as ** along with 4 people bicko chad_davis choonpeng martainn
  • notes ArchPRED: a template based loop structure prediction server.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by N Fernandez-Fuentes, J Zhai, A Fiser
    posted to fiser loop_modeling server structure_prediction by vavi on 2006-07-24 09:18:59 as *** along with 2 people eckart_bindewald cdeane
  • notes The Bioinformatics Template Library--generic components for biocomputing.
    Bioinformatics, Vol. 17, No. 8. (August 2001), pp. 729-737.
    by WR Pitt, MA Williams, M Steven, B Sweeney, AJ Bleasby, DS Moss
    posted to bioinformatics programming by vavi on 2006-07-17 18:41:25 as **
  • Dynamic contact maps of protein structures
    Journal of Molecular Graphics and Modelling, Vol. 16, No. 1. (February 1998), pp. 1-5.
    by Erik L Sonnhammer, John C Wootton
    posted to contact_map visualization by vavi on 2006-07-17 09:25:56 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • The Protein Data Bank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.
    by HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne
    posted to database pdb by vavi on 2006-07-17 09:09:40 as ** along with 22 people and 4 groups sebk higueruelo boris_aguilar nigham lillekatt thaliana dimka kuhn jwm bicko itmeson dgront caporaso condon leelarcombe aengisch debatebob massivemayhem gisle girschick selrac tji Radiation_Damage Stressosome biomedical-nlp beta
  • Sequence alignment approach to pick up conformationally similar protein fragments.
    J Mol Biol, Vol. 223, No. 4. (20 February 1992), pp. 1053-1061.
    by AS Kolaskar, U Kulkarni-Kale
    posted to sequence_alignment substitution_matrix by vavi on 2006-07-16 16:35:06 as **
  • 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 sequence_alignment by vavi on 2006-07-16 11:17:34 as * along with 8 people newton1234 creswick bicko dgront rabio cjeans incovoma sujaikumar
  • An improved algorithm for matching biological sequences.
    J Mol Biol, Vol. 162, No. 3. (15 December 1982), pp. 705-708.
    by O Gotoh
    posted to sequence_alignment by vavi on 2006-07-16 11:01:49 as ** along with 2 people adijr jofiel
  • A polynomial-time algorithm for the matching of crossing contact-map patterns
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 1, No. 4. (2004), pp. 171-180.
    by J Gramm
    posted to contact_map by vavi on 2006-07-03 16:31:45 as **
  • A Branch-and-Reduce Algorithm for the Contact Overlap Problem
    by Wie Xie
    posted to contact_map contact_map_overlap by vavi on 2006-07-03 16:17:46 as ****
  • Topology fingerprint approach to the inverse protein folding problem.
    J Mol Biol, Vol. 227, No. 1. (5 September 1992), pp. 227-238.
    by A Godzik, A Kolinski, J Skolnick
    posted to contact_map by vavi on 2006-07-03 10:12:16 as ** along with 3 people and 2 groups ana dgront rabio structural_bioinformatics Bioinformatics
  • notes Measuring the similarity of protein structures by means of the universal similarity metric.
    Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1015-1021.
    by N Krasnogor, DA Pelta
    posted to contact_maps structure_comparison by vavi on 2006-07-02 14:54:58 as ** along with 4 people and 2 groups ana okarsligil rabio rsantana structural_bioinformatics Bioinformatics
  • Protein fold recognition and dynamics in the space of contact maps
    Proteins: Structure, Function, and Genetics, Vol. 26, No. 4. (1996), pp. 391-410.
    by Leonid Mirny, Eytan Domany
    posted to contact_maps structure_prediction by vavi on 2006-07-02 13:37:50 as **
  • 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 contact_map contact_map_similarity structure_comparison by vavi on 2006-06-27 17:06:09 as *** along with 2 people and 2 groups carlk ana structural_bioinformatics Bioinformatics
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