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vavi's library [100 articles]

Recent papers added to vavi's library ordered by importance.
  • 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 ****
  • PDB-based protein loop prediction: parameters for selection and methods for optimization
    Journal of Molecular Biology, Vol. 267, No. 4. (11 April 1997), pp. 975-1001.
    by Herman W van Vlijmen, Martin Karplus
    posted to fragments library loop prediction by vavi on 2005-10-06 10:22:31 as ****
  • Structural similarity of loops in protein families: toward the understanding of protein evolution.
    BMC Evol Biol, Vol. 5, No. 1. (3 February 2005)
    by AR Panchenko, T Madej
    posted to loops similarity structure by vavi on 2005-08-24 13:50:56 as **** along with 1 person and 1 group Einat structural_bioinformatics
  • 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
  • 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
  • 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 ana carlk structural_bioinformatics Bioinformatics
  • Reconstruction of protein structures from a vectorial representation.
    Phys Rev Lett, Vol. 92, No. 21. (28 May 2004)
    by M Porto, U Bastolla, HE Roman, M Vendruscolo
    posted to contact_map structure_comparison structure_prediction by vavi on 2006-06-27 15:48:24 as *** along with 1 person dgront
  • Discrete restraint-based protein modeling and the Calpha-trace problem
    Protein Sci, Vol. 12, No. 9. (1 September 2003), pp. 2032-2046.
    by Mark A Depristo, Paul I de Bakker, Reshma P Shetty, Tom L Blundell
    posted to no-tag by vavi on 2006-06-23 13:05:22 as *** along with 2 people dgront medic0747
  • Recent developments in structural proteomics for protein structure determination.
    Proteomics, Vol. 5, No. 8. (May 2005), pp. 2056-2068.
    by HL Liu, JP Hsu
    posted to protein_structure_prediction survey by vavi on 2006-04-20 12:30:16 as *** along with 3 people eravikrishnan aqeel higueruelo
  • Capturing expert knowledge with argumentation: a case study in bioinformatics
    Bioinformatics, Vol. 22, No. 8. (15 April 2006), pp. 924-933.
    by Benjamin R Jefferys, Lawrence A Kelley, Marek J Sergot, John Fox, Michael J Sternberg
    posted to argumentation bioinformatics expert_knowledge by vavi on 2006-04-02 12:18:53 as *** along with 3 people and 2 groups mdimmic marcius eweaver BioinfoCIPF SGU-CIPF
  • Ab initio modeling of small, medium, and large loops in proteins
    Peptide Science, Vol. 60, No. 2. (6 July 2001), pp. 153-168.
    by Stan Galaktionov, Gregory V Nikiforovich, Garland R Marshall
    posted to ab_initio contact_map loop_prediction protein by vavi on 2005-11-07 15:54:00 as ***
  • Algorithmic Aspects of Protein Structure Similarity
    (1999)
    by Deborah Goldman, Christos H Papadimitriou, Sorin Istrail
    posted to algorithm protein structure_similarity by vavi on 2005-10-23 14:32:30 as ***
  • Protein loop structure prediction with flexible stem geometries.
    Proteins (12 October 2005)
    by M Mönnigmann, C A A Floudas
    posted to loop protein structure_prediction by vavi on 2005-10-20 13:19:50 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Network Analysis of Protein Structures Identifies Functional Residues
    Journal of Molecular Biology, Vol. 344, No. 4. (3 December 2004), pp. 1135-1146.
    by Gil Amitai, Arye Shemesh, Einat Sitbon, Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski
    posted to closeness residue_property by vavi on 2005-10-16 15:39:06 as *** along with 7 people and 1 group chrn bicko Einat amitai sriram_s massivemayhem siebertm structural_bioinformatics
  • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871.
    by Philip Bradley, Kira M Misura, David Baker
    posted to prediction structure by vavi on 2005-09-19 08:29:33 as *** along with 8 people and 4 groups BragilMassoud ana barry thaliana jwm marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.
    Protein Sci, Vol. 1, No. 2. (February 1992), pp. 216-226.
    by J Overington, D Donnelly, MS Johnson, A Sali, TL Blundell
    posted to acid amino matrix substitution by vavi on 2005-08-16 12:52:18 as *** along with 4 people and 1 group bicko Einat massivemayhem medic0747 structural_bioinformatics
  • EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
    BMC Bioinformatics, Vol. 6, No. 1. (10 January 2005)
    by JC Gelly, L Chiche, J Gracy
    posted to matrix prediction structure substitution by vavi on 2005-08-16 12:21:49 as *** along with 1 person rabio
  • 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 thaliana jwm bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
  • 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 24 people and 6 groups jmetzen MosesCheckley ldietz dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos cdeane haiyeong AbnerCYH isimpson jyuh nherveg 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
  • 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
  • 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 ana jwm wouterboomsma j3xucite hmk mijam joule 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 dgront rabio sekmi mijam mcbla
  • 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 dimka bicko chad_davis ttjoseph skhadar dgront rabio massivemayhem medic0747 sebk granujilla
  • 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 iakes cdeane saunders
  • 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 dimka wouterboomsma mijam j3xucite
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