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mirzazadehs library [58 articles]

Nye artikler sendt til mirzazadehs bibliotek.
  • Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.
    J Comput Chem, Vol. 25, No. 5. (15 April 2004), pp. 712-724.
    by E Eyal, R Najmanovich, BJ McConkey, M Edelman, V Sobolev
    posted to no-tag by mirzazadeh on 2007-04-22 15:59:37 as ** along with 2 people j3xucite blackbart
  • Environment-dependent residue contact energies for proteins
    PNAS, Vol. 97, No. 6. (14 March 2000), pp. 2550-2555.
    by Chao Zhang, Sung-Hou Kim
    posted to no-tag by mirzazadeh on 2007-04-22 15:58:43 as **
  • An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes
    Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259.
    by Tanja Kortemme, Alexandre V Morozov, David Baker
    posted to no-tag by mirzazadeh on 2007-04-22 15:57:35 as ** along with 1 person hmk
  • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.
    Protein Sci, Vol. 13, No. 2. (February 2004), pp. 400-411.
    by C Zhang, S Liu, H Zhou, Y Zhou
    posted to no-tag by mirzazadeh on 2007-04-22 15:56:23 as ** along with 2 people j3xucite kgutwin
  • Development of novel statistical potentials for protein fold recognition.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 225-232.
    by NV Buchete, JE Straub, D Thirumalai
    posted to no-tag by mirzazadeh on 2007-04-22 15:55:45 as ** along with 1 person thamelry
  • 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 no-tag by mirzazadeh on 2007-04-22 15:54:17 as ** along with 2 people eweaver rabio
  • Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction.
    Protein Sci, Vol. 9, No. 7. (July 2000), pp. 1399-1401.
    by R Samudrala, M Levitt
    posted to no-tag by mirzazadeh on 2007-04-22 15:51:41 as ** along with 1 person aengisch
  • Sequencing-by-hybridization at the information-theory bound: an optimal algorithm.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 621-630.
    by FP Preparata, E Upfal
    posted to no-tag by mirzazadeh on 2007-04-22 15:50:36 as **
  • Fast de novo peptide sequencing and spectral alignment via tree decomposition.
    Pac Symp Biocomput (2006), pp. 255-266.
    by C Liu, Y Song, B Yan, Y Xu, L Cai
    posted to no-tag by mirzazadeh on 2007-04-22 15:48:17 as ** along with 1 person nedwards
  • Cooperativity in protein-folding kinetics.
    Proc Natl Acad Sci U S A, Vol. 90, No. 5. (1 March 1993), pp. 1942-1946.
    by KA Dill, KM Fiebig, HS Chan
    posted to no-tag by mirzazadeh on 2007-04-22 15:45:57 as **
  • An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs
    Journal of Computational Chemistry, Vol. 24, No. 2. (2003), pp. 222-231.
    by Robert J Petrella, Ioan Andricioaei, Bernard R Brooks, Martin Karplus
    posted to no-tag by mirzazadeh on 2007-03-31 02:32:00 as read along with 2 people dgront blackbart
  • Protein folding and chart parsing
    (2006), pp. 293-300.
    by Julia Hockenmaier, Aravind K Joshi, Ken A Dill
    posted to no-tag by mirzazadeh on 2007-03-25 00:28:48 as **
  • Empirical force fields for biological macromolecules: Overview and issues
    Journal of Computational Chemistry, Vol. 25, No. 13. (1 July 2004), pp. 1584-1604.
    by Alexander D Mackerell
    posted to no-tag by mirzazadeh on 2007-03-23 17:37:22 as ** along with 5 people and 2 groups BragilMassoud marcius dgront loison AndreaColetta BioinfoCIPF SGU-CIPF
  • 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 no-tag by mirzazadeh on 2007-03-23 14:21:28 as ** along with 13 people and 3 groups thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
  • Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
    Current Opinion in Structural Biology, Vol. 14, No. 2. (April 2004), pp. 233-241.
    by Anne Poupon
    posted to no-tag by mirzazadeh on 2007-03-22 15:31:44 as ** along with 3 people apaydin aengisch siebertm
  • Discrimination of native protein structures using atom-atom contact scoring.
    Proc Natl Acad Sci U S A, Vol. 100, No. 6. (18 March 2003), pp. 3215-3220.
    by BJ McConkey, V Sobolev, M Edelman
    posted to no-tag by mirzazadeh on 2007-03-20 13:12:34 as **
  • Free modeling with Rosetta in CASP6.
    Proteins (26 September 2005)
    by Philip Bradley, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David E E Kim, Jens Meiler, Kira M S M Misura, David Baker
    posted to no-tag by mirzazadeh on 2007-03-19 16:02:46 as ** along with 4 people and 2 groups jwm marcius dgront schuylrp BioinfoCIPF SGU-CIPF
  • Local matching of random restriction maps
    Journal of applied probability, Vol. 38, No. 2. (2001), pp. 335-356.
    by Mengxiang Tang, Waterman
    posted to no-tag by mirzazadeh on 2007-03-19 14:33:12 as **
  • Practical lessons from protein structure prediction.
    Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891.
    by K Ginalski, NV Grishin, A Godzik, L Rychlewski
    posted to no-tag by mirzazadeh on 2007-03-17 21:48:02 as ** along with 7 people and 4 groups ana aalibes thaliana okarsligil marcius duartemolha dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Enhanced Sequence Reconstruction with DNA Microarray Application
    (2001), pp. 64-74.
    by Samuel A Heath, Franco P Preparata
    posted to no-tag by mirzazadeh on 2007-03-17 21:29:06 as **
  • Optimal Probing Patterns for Sequencing by Hybridization
    : Algorithms in Bioinformatics (2006), pp. 366-375.
    by Dekel Tsur
    posted to no-tag by mirzazadeh on 2007-03-17 21:27:36 as **
  • Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction
    : Algorithms in Bioinformatics (2006), pp. 219-230.
    by Eun-Jong Hong, Tomã¡s Lozano-Pã©rez
    posted to no-tag by mirzazadeh on 2007-03-17 21:25:48 as **
  • MAP estimation via agreement on trees: message-passing and linear programming
    Information Theory, IEEE Transactions on, Vol. 51, No. 11. (2005), pp. 3697-3717.
    by MJ Wainwright, TS Jaakkola, AS Willsky
    posted to no-tag by mirzazadeh on 2007-03-17 21:19:44 as ** along with 1 person pcarbo
  • On the power of universal bases in sequencing by hybridization
    (1999), pp. 295-301.
    by Franco P Preparata, Alan M Frieze, Eli Upfal
    posted to no-tag by mirzazadeh on 2007-03-17 21:12:18 as **
  • Alignment of metabolic pathways
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3401-3408.
    by Ron Y Pinter, Oleg Rokhlenko, Esti Yeger-Lotem, Michal Ziv-Ukelson
    posted to no-tag by mirzazadeh on 2007-03-17 21:11:11 as ** along with 2 people zmasek carlk
  • Reducing Distortion in Phylogenetic Networks
    : Algorithms in Bioinformatics (2006), pp. 150-161.
    by Daniel H Huson, Mike A Steel, Jim Whitfield
    posted to no-tag by mirzazadeh on 2007-03-17 12:43:34 as **
  • Alignment with Non-overlapping Inversions in O(n3)-Time
    : Algorithms in Bioinformatics (2006), pp. 186-196.
    by Augusto F Vellozo, Carlos ER Alves, Alair
    posted to no-tag by mirzazadeh on 2007-03-17 12:39:54 as **
  • On the Complexity of the Crossing Contact Map Pattern Matching Problem
    : Algorithms in Bioinformatics (2006), pp. 231-241.
    by Shuai C Li, Ming Li
    posted to no-tag by mirzazadeh on 2007-03-17 12:09:28 as **
  • Modeling of loops in protein structures.
    Protein Sci, Vol. 9, No. 9. (September 2000), pp. 1753-1773.
    by A Fiser, RK Do, A Sali
    posted to no-tag by mirzazadeh on 2007-03-17 12:05:33 as ** along with 4 people warlock6x3 vavi ttjoseph tji
  • Fold recognition via a tree.
    J Comput Biol, Vol. 13, No. 9. (November 2006), pp. 1565-1573.
    by Y Chen, GM Crippen
    posted to no-tag by mirzazadeh on 2007-03-17 01:29:53 as **
  • Are Proteins Well-Packed?
    Biophys. J., Vol. 81, No. 2. (1 August 2001), pp. 751-766.
    by Jie Liang, Ken A Dill
    posted to no-tag by mirzazadeh on 2007-03-17 01:21:09 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • PROSPECT II: protein structure prediction program for genomescale applications
    pp. 641-650.
    by Dongsup Kim
    posted to no-tag by mirzazadeh on 2007-03-17 01:19:26 as **
  • The present view of the mechanism of protein folding.
    Nat Rev Mol Cell Biol, Vol. 4, No. 6. (June 2003), pp. 497-502.
    by V Daggett, A Fersht
    posted to no-tag by mirzazadeh on 2007-03-17 01:12:58 as ** along with 3 people and 2 groups ana okarsligil bilab structural_bioinformatics Bioinformatics
  • The Pfam protein families database.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 276-280.
    by A Bateman, E Birney, L Cerruti, R Durbin, L Etwiller, SR Eddy, S Griffiths-Jones, KL Howe, M Marshall, EL Sonnhammer
    posted to no-tag by mirzazadeh on 2007-03-17 01:12:09 as ** along with 9 people and 1 group tharris ziquje Cortel cjeans wenhan antonkratz IrinaMoreira bandrewfox gulkur C. elegans / WormBase
  • Prediction of Hydrophobic Cores of Proteins Using Wavelet Analysis.
    Genome Inform Ser Workshop Genome Inform, Vol. 8 (1997), pp. 61-70.
    by H Hirakawa, S Kuhara
    posted to no-tag by mirzazadeh on 2007-03-17 01:11:20 as **
  • TASSER: An automated method for the prediction of protein tertiary structures in CASP6.
    Proteins (26 September 2005)
    by Yang Zhang, Adrian K K Arakaki, Jeffrey Skolnick
    posted to no-tag by mirzazadeh on 2007-03-16 23:48:57 as ** along with 4 people and 2 groups nigham marcius dgront schuylrp BioinfoCIPF SGU-CIPF
  • Fold recognition by combining profile-profile alignment and support vector machine
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2667-2673.
    by Sangjo Han, Byung-Chul Lee, Seung T Yu, Chan-Seok Jeong, Soyoung Lee, Dongsup Kim
    posted to no-tag by mirzazadeh on 2007-03-16 23:45:30 as ** along with 1 person j3xucite
  • Protein structure prediction and structural genomics.
    Science, Vol. 294, No. 5540. (5 October 2001), pp. 93-96.
    by D Baker, A Sali
    posted to no-tag by mirzazadeh on 2007-03-16 22:34:28 as read along with 7 people and 2 groups ana vavi dgront sriram_s mingzhi granujilla janasont structural_bioinformatics Bioinformatics
  • A Tutorial on Spectral Clustering
    by Ulrike von Luxburg
    posted to no-tag by mirzazadeh on 2007-03-16 16:05:05 as **
  • Is there a unifying mechanism for protein folding?
    Trends Biochem Sci, Vol. 28, No. 1. (January 2003), pp. 18-25.
    by V Daggett, AR Fersht
    posted to no-tag by mirzazadeh on 2007-03-16 16:03:02 as ** along with 4 people and 1 group Einat dgront allmensch rabio structural_bioinformatics
  • Rosetta in CASP4: progress in ab initio protein structure prediction.
    Proteins, Vol. Suppl 5 (2001), pp. 119-126.
    by R Bonneau, J Tsai, I Ruczinski, D Chivian, C Rohl, CE Strauss, D Baker
    posted to no-tag by mirzazadeh on 2007-03-16 00:47:28 as **
  • Automated structure prediction of weakly homologous proteins on a genomic scale
    PNAS, Vol. 101, No. 20. (18 May 2004), pp. 7594-7599.
    by Yang Zhang, Jeffrey Skolnick
    posted to no-tag by mirzazadeh on 2007-03-16 00:45:04 as ** along with 3 people nigham wouterboomsma j3xucite
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to no-tag by mirzazadeh on 2007-03-16 00:44:06 as ** along with 46 people and 4 groups pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • From molecular to modular cell biology.
    Nature, Vol. 402, No. 6761 Suppl. (2 December 1999)
    by LH Hartwell, JJ Hopfield, S Leibler, AW Murray
    posted to no-tag by mirzazadeh on 2007-03-15 23:04:28 as ** along with 17 people and 8 groups AurelienMazurie rhem1224 balajis nuke2005 rubendrr wnpx i41m adepace javierFellow mmt carmaus dejori carlk awooga tvdbulck vsausg dragonrez EisenLab TCR_Signaling cytoskeleton-and-afm SysbioMPI-TCells dIEMoSIRIS ic4 generif_paper MoSi-Rostock
  • Pairwise contact potentials are unsuitable for protein folding
    J. Chem. Phys., Vol. 109 (December 1998), pp. 11101-11108.
    by M Vendruscolo, E Domany
    posted to no-tag by mirzazadeh on 2007-03-15 23:03:52 as **
  • Conserved pathways within bacteria and yeast as revealed by global protein network alignment.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11394-11399.
    by BP Kelley, R Sharan, RM Karp, T Sittler, DE Root, BR Stockwell, T Ideker
    posted to no-tag by mirzazadeh on 2007-03-15 23:01:59 as ** along with 9 people and 1 group emmackinnon okarsligil balajis nuke2005 gurkanbebek denilw shu mdstobbe carlk Bioinformatics
  • A surprising simplicity to protein folding.
    Nature, Vol. 405, No. 6782. (4 May 2000), pp. 39-42.
    by D Baker
    posted to no-tag by mirzazadeh on 2007-03-15 23:00:41 as ** along with 4 people and 1 group imouthesmp Einat gbart phoenixzxl structural_bioinformatics
  • Pairwise Alignment of Protein Interaction Networks
    JOURNAL OF COMPUTATIONAL BIOLOGY
    posted to no-tag by mirzazadeh on 2007-03-15 22:59:16 as **
  • Modular organization of protein interaction networks
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 207-214.
    by Luo, Feng, Yang, Yunfeng, Chen, Chin-Fu, Chang, Roger, Zhou, Jizhong, Scheuermann, H Richard
    posted to no-tag by mirzazadeh on 2007-03-15 22:56:27 as **
  • Detecting conserved interaction patterns in biological networks.
    J Comput Biol, Vol. 13, No. 7. (September 2006), pp. 1299-1322.
    by M Koyutürk, Y Kim, S Subramaniam, W Szpankowski, A Grama
    posted to no-tag by mirzazadeh on 2007-03-15 22:55:29 as ** along with 2 people and 1 group balajis massivemayhem Bioinformatics
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