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rabio library [307 articles]

Статьи, недавно добавленные в библиотеку rabio .
  • Streaming XML with Jabber/XMPP
    IEEE Internet Computing, Vol. 9, No. 5. (September 2005), pp. 82-89.
    by Peter Saint-Andre
    posted to xmpp jabber by rabio on 2008-07-11 16:56:05 as **
  • The Quaternions with Applications to Rigid Body Dynamics; Sandia National Laboratories
    (2004)
    by Evangelos A Coutsias, Louis Romero
    posted to quaternions by rabio on 2008-06-04 18:15:13 as **
  • A solution to the weighted procrustes problem in which the transformation is in agreement with the loss function
    Psychometrika, Vol. 41, No. 4. (18 December 1976), pp. 547-550.
    by Robert Lissitz, Peter Schönemann, James Lingoes
    posted to svd rmsd algebra by rabio on 2008-05-05 23:54:18 as **
  • A generalized solution of the orthogonal procrustes problem
    Psychometrika, Vol. 31, No. 1. (27 March 1966), pp. 1-10.
    by Peter Schönemann
    posted to svd rmsd algebra by rabio on 2008-05-05 22:23:42 as **
  • CDD: a Conserved Domain Database for protein classification
    Nucleic Acids Research, Vol. 33, No. Database issue. (1 January 2005), pp. D192-196.
    by Aron M Bauer, John B Anderson, Praveen F Cherukuri, Carol D Scott, Lewis Y Geer, Marc Gwadz, Siqian He, David I Hurwitz, John D Jackson, Zhaoxi Ke, Christopher J Lanczycki, Cynthia A Liebert, Chunlei Liu, Fu Lu, Gabriele H Marchler, Mikhail Mullokandov, Benjamin A Shoemaker, Vahan Simonyan, James S Song, Paul A Thiessen, Roxanne A Yamashita, Jodie J Yin, Dachuan Zhang, Stephen H Bryant
    posted to database by rabio on 2008-04-27 12:24:36 as ** along with 2 people balajis cjeans
  • Dictionary of recurrent domains in protein structures
    Proteins: Structure, Function, and Genetics, Vol. 33, No. 1. (1998), pp. 88-96.
    by Liisa Holm, Chris Sander
    posted to structure_alignment structure_comparison by rabio on 2008-04-17 14:19:57 as **
  • ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.
    BMC Bioinformatics, Vol. 7 (April 2006), 206.
    by V Sam, CH Tai, J Garnier, JF Gibrat, B Lee, PJ Munson
    posted to structure_comparison by rabio on 2008-04-14 19:41:51 as ** along with 1 person karbak
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to structure_predition by rabio on 2008-04-14 19:28:05 as ** along with 4 people chad_davis mkurc zwang mclarenv
  • DaliLite workbench for protein structure comparison
    Bioinformatics, Vol. 16, No. 6. (1 June 2000), pp. 566-567.
    by Liisa Holm, Jong Park
    posted to structure_alignment structure_comparison by rabio on 2008-04-14 19:17:48 as ** along with 1 person sim82
  • MUSTANG: A multiple structural alignment algorithm
    Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 3. (2006), pp. 559-574.
    by Arun S Konagurthu, James C Whisstock, Peter J Stuckey, Arthur M Lesk
    posted to multiple_sequence_alignment structure_alignment by rabio on 2008-04-08 10:33:44 as ** along with 4 people and 3 groups karbak ana jwm Thaverkamp structural_bioinformatics Bioinformatics Microbial-Ecology
  • SuperPose: a simple server for sophisticated structural superposition.
    Nucleic Acids Research, Vol. 32, No. Web Server Issue. (1 July 2004), pp. W590-W594.
    by R Maiti, GH Van Domselaar, H Zhang, DS Wishart
    posted to no-tag by rabio on 2008-04-01 02:35:00 as * along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Covariance weighted Procrustes analysis
    (4-6 July 2005), pp. 107-110.
    by Christopher J Brignell, William J Browne, Ian L Dryden
    edited by S Barber, PD Baxter, KV Mardia, RE Walls
    posted to rmsd by rabio on 2008-04-01 02:32:17 as **
  • Comment on 'Using quaternions to calculate RMSD' [J. Comp. Chem. 25, 1849 (2004)]
    Journal of Computational Chemistry, Vol. 26 (June 2005), pp. 1660-1662.
    by GR Kneller
    posted to rmsd structure_comparison by rabio on 2008-04-01 02:00:05 as **
  • Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller
    Journal of Computational Chemistry, Vol. 26, No. 15. (2005), pp. 1663-1665.
    by Evangelos A Coutsias, Chaok Seok, Ken A Dill
    posted to rmsd structure_comparison by rabio on 2008-04-01 01:49:24 as **
  • Using quaternions to calculate RMSD
    Journal of Computational Chemistry, Vol. 25, No. 15. (30 November 2004), pp. 1849-1857.
    by Evangelos A Coutsias, Choak Seok, Ken A Dill
    posted to rmsd structure_comparison by rabio on 2008-03-31 16:58:56 as *** along with 4 people BragilMassoud apaydin nachtalp dgront
  • The structural alignment between two proteins: is there a unique answer?
    Protein Science : a Publication of the Protein Society, Vol. 5, No. 7. (July 1996), pp. 1325-1338.
    by A Godzik
    posted to structure_alignment by rabio on 2008-03-31 01:41:46 as ** along with 3 people and 2 groups ana j3xucite Inchoate structural_bioinformatics Bioinformatics
  • RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
    Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 15-21.
    by Tim JP Hubbard
    posted to casp rmsd by rabio on 2008-03-31 01:35:32 as **
  • Matrix computations (3rd ed.)
    (1996)
    by Gene H Golub, Charles F Van Loan
    posted to algebra book computation numerical by rabio on 2008-03-30 22:15:25 as ** along with 1 person chandlerc
  • Utility library for structural bioinformatics
    Bioinformatics, Vol. 24, No. 4. (28 January 2008), pp. 584-585.
    by Dominik Gront, Andrzej Kolinski
    posted to tools by rabio on 2008-03-30 22:01:59 as read along with 3 people chad_davis dgront Minty
  • Rotational superposition: a review of methods
    Journal of Molecular Graphics & Modelling, Vol. 17, No. 3-4. (g 1999), pp. 238-244.
    by Darren R Flower
    posted to review rmsd structure_comparison by rabio on 2008-03-30 21:37:58 as read
  • A note on the rotational superposition problem
    Acta Crystallographica Section A, Vol. 44, No. 2. (Mar 1988), pp. 211-216.
    by Robert Diamond
    posted to rmsd structure_comparison by rabio on 2008-03-30 14:15:23 as ***
  • On the multiple simultaneous superposition of molecular structures by rigid body transformations
    Protein Science : a Publication of the Protein Society, Vol. 1, No. 10. (1 October 1992), pp. 1279-1287.
    by Robert Diamond
    posted to rmsd structure_comparison by rabio on 2008-03-29 23:28:46 as **
  • Predicting absolute contact numbers of native protein structure from amino acid sequence.
    Proteins, Vol. 58, No. 1. (1 January 2005), pp. 158-165.
    by AR Kinjo, K Horimoto, K Nishikawa
    posted to 1-d_structure contacts_number_prediction by rabio on 2008-03-27 10:35:42 as *** along with 1 person kirasato
  • Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks
    Biophysics, Vol. 1 (2005), pp. 67-74.
    by Akira R Kinjo, Ken Nishikawa
    posted to secondary_structure by rabio on 2008-03-25 17:51:25 as **
  • Recoverable one-dimensional encoding of three-dimensional protein structures
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2167-2170.
    by Akira R Kinjo, Ken Nishikawa
    posted to secondary_structure by rabio on 2008-03-25 17:44:38 as ** along with 2 people eweaver mirzazadeh
  • CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
    BMC Bioinformatics, Vol. 7 (05 September 2006), 401.
    by Akira R Kinjo, Ken Nishikawa
    posted to 1-d_structure secondary_structure by rabio on 2008-03-25 17:40:15 as **
  • Protein Sequence Alignment and Database Scanning
    (1996)
    by Geoffrey J Barton
    edited by MJE Sternberg
    posted to sequence_alignment by rabio on 2008-03-25 15:53:50 as **
  • Ultra-fast Matrix Multiplication: An Empirical Analysis of Highly Optimized Vector Algorithm
    Stanford Undergraduate Research Journal (SURJ), Vol. 3 (2004), pp. 33-36.
    by Boyko Kakaradov
    posted to algebra by rabio on 2008-03-25 14:39:20 as **
  • On the Early History of the Singular Value Decomposition
    SIAM Review, Vol. 35, No. 4. (1993), pp. 551-566.
    by GW Stewart
    posted to algebra svd by rabio on 2008-03-24 12:59:09 as **
  • Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures
    Biophysical Journal, Vol. 90, No. 12. (15 June 2006), pp. 4558-4573.
    by Kelly L Damm, Heather A Carlson
    posted to rmsd structure_comparison by rabio on 2008-03-23 17:37:20 as read along with 3 people higueruelo blackbart choonpeng
  • Metric properties of the root-mean-square deviation of vector sets
    Acta Crystallographica Section A, Vol. 53, No. 6. (November 1997)
    by K Kaindl, B Steipe
    posted to metric rmsd by rabio on 2008-03-23 16:56:35 as read
  • A Study on Tools and Algorithms for 3-D Protein Structures Alignment and Comparison
    (12-17 December 2004), pp. 1000-1005.
    by Ying H Lin, Hsun C Chang, Yaw L Lin
    posted to structure_alignment structure_comparison by rabio on 2008-03-21 13:13:34 as **
  • Computational Analysis of Sequence Selection Mechanisms
    Structure (London, England : 1993), Vol. 12, No. 4. (April 2004), pp. 547-557.
    by Leonid Meyerguz, Catherine Grasso, Jon Kleinberg, Ron Elber
    posted to no-tag by rabio on 2008-03-21 11:46:50 as ** along with 1 person apaydin
  • A solution for the best rotation to relate two sets of vectors
    Acta Crystallographica Section A, Vol. 32, No. 5. (September 1976), pp. 922-923.
    by W Kabsch
    posted to rmsd structure_comparison by rabio on 2008-03-21 11:32:44 as ***
  • A discussion of the solution for the best rotation to relate two sets of vectors
    Acta Crystallographica Section A, Vol. 34, No. 5. (September 1978), pp. 827-828.
    by W Kabsch
    posted to rmsd structure_comparison by rabio on 2008-03-21 11:30:44 as ***
  • Practical conversion from torsion space to Cartesian space for in silico protein synthesis
    Journal of Computational Chemistry, Vol. 26, No. 10. (30 July 2005), pp. 1063-1068.
    by Jerod Parsons, Bradley J Holmes, Maurice J Rojas, Jerry Tsai, Charlie EM Strauss
    posted to internal_coordinates by rabio on 2008-03-20 12:36:41 as ** along with 1 person dgront
  • Calculating the Singular Values and Pseudo-Inverse of a Matrix
    Journal of the Society for Industrial and Applied Mathematics, Series B: Numerical Analysis, Vol. 2, No. 2. (1965), pp. 205-224.
    by G Golub, W Kahan
    posted to algebra numerical svd by rabio on 2008-02-06 15:25:22 as **
  • Exploiting the past and the future in protein secondary structure prediction
    Bioinformatics, Vol. 15, No. 11. (November 1999), pp. 937-946.
    by Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri
    posted to secondary_structure by rabio on 2008-02-02 11:05:16 as ** along with 3 people and 1 group girschick dgront paolo Bioinformatics
  • Alignments grow, secondary structure prediction improves
    Proteins: Structure, Function, and Genetics, Vol. 46, No. 2. (2002), pp. 197-205.
    by Dariusz Przybylski, Burkhard Rost
    posted to secondary_structure by rabio on 2008-01-31 16:13:42 as read along with 1 person yoonk
  • The Principled Design of Large-Scale Recursive Neural Network Architectures–DAG-RNNs and the Protein Structure Prediction Problem
    Journal of Machine Learning Research, Vol. 4, No. 4. (15 May 2004), pp. 575-602.
    by Pierre Baldi, Gianluca Pollastri
    posted to no-tag by rabio on 2008-01-31 15:53:51 as **
  • SCRATCH: a protein structure and structural feature prediction server
    Nucleic Acids Research, Vol. 33, No. Web Server Issue. (March 2005), pp. W72-W76.
    by J Cheng, AZ Randall, MJ Sweredoski, P Baldi
    posted to secondary_structure by rabio on 2008-01-31 15:35:14 as **
  • Prediction of protein conformational freedom from distance constraints
    Proteins: Structure, Function, and Genetics, Vol. 29, No. 2. (7 December 1998), pp. 240-251.
    by BL de Groot, DMF van Aalten, RM Scheek, A Amadei, G Vriend, HJC Berendsen
    posted to algorithms conformation by rabio on 2008-01-19 11:15:50 as ** along with 5 people and 2 groups aqeel yhu dgront superpyrin mijam TSRI_MGL Conformational_disease
  • Protein secondary structure prediction based on position-specific scoring matrices
    Journal of Molecular Biology, Vol. 292, No. 2. (17 September 1999), pp. 195-202.
    by David T Jones
    posted to secondary_structure tools by rabio on 2008-01-13 11:16:14 as ** along with 8 people saunders dandaman chad_davis wouterboomsma j3xucite dgront leelarcombe rph
  • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    Journal of Molecular Modeling, Vol. 7, No. 8. (2001), pp. 306-317.
    by Erik Lindahl, Berk Hess, David van der Spoel
    posted to molecular_dynamics tools by rabio on 2007-12-31 10:44:56 as ** along with 2 people and 2 groups roland_ewald tji dIEMoSIRIS MoSi-Rostock
  • Background frequencies for residue variability estimates: BLOSUM revisited
    BMC Bioinformatics, Vol. 8 (27 December 2007), 488.
    by I Mihalek, I Res, O Lichtarge
    posted to substitution_matrices by rabio on 2007-12-31 08:37:31 as *** along with 5 people and 1 group bicko chad_davis gokhan laughcry biehl structural_bioinformatics
  • Accuracy of structure-based sequence alignments of automatic methods
    BMC Bioinformatics, Vol. 8 (20 September 2007), 355.
    by Changhoon Kim, Byungkook Lee
    posted to sequence_alignment structure_alignment by rabio on 2007-12-31 02:58:24 as read along with 3 people dimka chad_davis zwang
  • GROMACS: fast, flexible, and free
    Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718.
    by D Van Der Spoel, E Lindahl, B Hess, G Groenhof, AE Mark, HJ Berendsen
    posted to molecular_dynamics tools by rabio on 2007-12-30 22:32:38 as ** along with 9 people and 2 groups robertvacha dimka jwm ttjoseph bilab Dinler tji softsimu ashaytan Radiation_Damage Stressosome
  • Gromacs User Manual version 3.3
    (2005)
    by David van der Spoel, Erik Lindahl, Berk Hess, Aldert R van Buuren, Emile Apol, Pieter J Meulenhoff, Peter D Tieleman, Alfons LTM Sijbers, Anton K Feenstra, Rudi van Drunen, Herman JC Berendsen
    posted to manual molecular_dynamics tools by rabio on 2007-12-30 22:07:48 as **
  • Multiple Hypothesis Testing
    Annual Review of Psychology, Vol. 46, No. 1. (1995), pp. 561-584.
    by Juliet P Shaffer
    posted to p-value review statistics by rabio on 2007-12-27 18:23:01 as *** along with 1 person kgajos
  • The Structure of the First Coordination Shell in Liquid Water
    Science, Vol. 304, No. 5673. (14 May 2004), pp. 995-999.
    by Ph Wernet, D Nordlund, U Bergmann, M Cavalleri, M Odelius, H Ogasawara, LA Naslund, TK Hirsch, L Ojamae, P Glatzel, LGM Pettersson, A Nilsson
    posted to nmr water by rabio on 2007-12-27 13:10:09 as ** along with 3 people and 1 group gane5h samjlord ruvido moernerlab
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