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aengischs library [37 articles]

Neue Artikel in aengischs Bibliothek.
  • A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics.
    J Mol Biol, Vol. 329, No. 1. (23 May 2003), pp. 159-174.
    by C Keasar, M Levitt
    posted to decoys by aengisch on 2007-02-12 13:51:36 as **
  • Scoring function for automated assessment of protein structure template quality
    Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 4., pp. 702-710.
    by Yang Zhang, Jeffrey Skolnick
    posted to tm-score by aengisch on 2007-02-05 11:35:33 as ** along with 5 people and 2 groups karbak marcius dgront rabio granujilla BioinfoCIPF SGU-CIPF
  • Critical assessment of methods of protein structure prediction (CASP)--round 6.
    Proteins, Vol. 61 Suppl 7 (2005), pp. 3-7.
    by J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano
    posted to casp6 by aengisch on 2007-02-05 11:07:09 as ** along with 4 people j3xucite dgront schuylrp saunders
  • Vorolign--fast structural alignment using Voronoi contacts.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by F Birzele, JE Gewehr, G Csaba, R Zimmer
    posted to adds by aengisch on 2007-02-04 10:25:58 as ** along with 2 people bicko siebertm
  • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.
    Macromolecules, Vol. 9, No. 6. (c 1976), pp. 945-950.
    by S Tanaka, HA Scheraga
    posted to intro by aengisch on 2007-02-01 20:50:54 as ** along with 4 people and 2 groups ana thaliana dgront mcbla structural_bioinformatics Bioinformatics
  • A simplified amino acid potential for use in structure predictions of proteins.
    Proteins, Vol. 18, No. 3. (March 1994), pp. 267-280.
    by A Wallqvist, M Ullner
    posted to intro by aengisch on 2007-02-01 20:48:33 as **
  • Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models.
    J Mol Biol, Vol. 247, No. 5. (14 April 1995), pp. 995-1012.
    by A Monge, EJ Lathrop, JR Gunn, PS Shenkin, RA Friesner
    posted to intro by aengisch on 2007-02-01 16:00:02 as **
  • Reduced protein models and their application to the protein folding problem.
    J Biomol Struct Dyn, Vol. 16, No. 2. (October 1998), pp. 381-396.
    by J Skolnick, A Kolinski, AR Ortiz
    posted to intro by aengisch on 2007-02-01 15:57:08 as **
  • TM-align: a protein structure alignment algorithm based on the TM-score.
    Nucleic Acids Res, Vol. 33, No. 7. (2005), pp. 2302-2309.
    by Y Zhang, J Skolnick
    posted to adds by aengisch on 2007-01-31 16:07:58 as ** along with 1 person j3xucite
  • The ASTRAL Compendium in 2004.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by JM Chandonia, G Hon, NS Walker, L Lo Conte, P Koehl, M Levitt, SE Brenner
    posted to adds by aengisch on 2007-01-31 12:47:13 as ** along with 6 people chad_davis sriram_s rabio siebertm saunders reyez
  • SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    J Mol Biol, Vol. 247, No. 4. (7 April 1995), pp. 536-540.
    by AG Murzin, SE Brenner, T Hubbard, C Chothia
    posted to adds by aengisch on 2007-01-31 12:45:32 as ** along with 10 people pjcite dimka chrn chad_davis j3xucite sriram_s massivemayhem cjeans siebertm sim82
  • 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 adds by aengisch on 2007-01-31 09:52:02 as ** along with 51 people and 4 groups daforerog nlapalu sebk tjimenez shung 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 rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • The Quickhull algorithm for convex hulls
    ACM Trans. on Mathematical Software, Vol. 22 (December 1996), pp. 469-483.
    by CB Barber, DP Dobkin, HT Huhdanpaa
    posted to adds by aengisch on 2007-01-31 09:47:19 as **
  • Voro3D: 3D Voronoi tessellations applied to protein structures.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1715-1716.
    by F Dupuis, JF Sadoc, R Jullien, B Angelov, JP Mornon
    posted to adds by aengisch on 2007-01-31 09:41:00 as ** along with 1 person siebertm
  • 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 adds by aengisch on 2007-01-31 09:37:35 as ** along with 24 people and 4 groups reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon leelarcombe debatebob massivemayhem gisle girschick selrac tji higueruelo boris_aguilar sebk timg Radiation_Damage Stressosome biomedical-nlp beta
  • Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
    Pac Symp Biocomput (1996), pp. 53-72.
    by NN Alexandrov, R Nussinov, RM Zimmer
    posted to 123d by aengisch on 2007-01-31 09:16:45 as ** along with 1 person chad_davis
  • in preparation
    (1999)
    by Kesar
    posted to decoys by aengisch on 2007-01-31 08:35:20 as **
  • Ab initio construction of protein tertiary structures using a hierarchical approach.
    J Mol Biol, Vol. 300, No. 1. (30 June 2000), pp. 171-185.
    by Y Xia, ES Huang, M Levitt, R Samudrala
    posted to decoys by aengisch on 2007-01-31 08:31:26 as ** along with 1 person j3xucite
  • A combined approach for ab initio construction of low resolution protein tertiary structures from sequence.
    Pac Symp Biocomput (1999), pp. 505-516.
    by R Samudrala, Y Xia, M Levitt, ES Huang
    posted to decoys by aengisch on 2007-01-31 08:30:49 as **
  • Energy functions that discriminate X-ray and near native folds from well-constructed decoys.
    J Mol Biol, Vol. 258, No. 2. (3 May 1996), pp. 367-392.
    by B Park, M Levitt
    posted to decoys by aengisch on 2007-01-31 08:28:49 as *
  • 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 decoys by aengisch on 2007-01-07 10:56:45 as ** along with 1 person mirzazadeh
  • Novel knowledge-based mean force potential at the profile level
    BMC Bioinformatics, Vol. 7 (27 June 2006), 324.
    by Qiwen Dong, Xiaolong Wang, Lei Lin
    posted to profiles by aengisch on 2006-12-28 10:44:41 as read along with 1 person j3xucite
  • Voronoï tessellation reveals the condensed matter character of folded proteins.
    Phys Rev Lett, Vol. 85, No. 16. (16 October 2000), pp. 3532-3535.
    by A Soyer, J Chomilier, JP Mornon, R Jullien, JF Sadoc
    posted to voronoi by aengisch on 2006-12-08 07:45:41 as **
  • Calculation of protein volumes: an alternative to the Voronoi procedure.
    J Mol Biol, Vol. 161, No. 2. (25 October 1982), pp. 305-322.
    by BJ Gellatly, JL Finney
    posted to voronoi by aengisch on 2006-12-08 07:44:36 as ** along with 2 people bicko siebertm
  • Calculation of molecular volumes and areas for structures of known geometry.
    Methods Enzymol, Vol. 115 (1985), pp. 440-464.
    by FM Richards
    posted to voronoi by aengisch on 2006-12-08 07:43:06 as **
  • Volume occupation, environment and accessibility in proteins. The problem of the protein surface.
    J Mol Biol, Vol. 96, No. 4. (25 August 1975), pp. 721-732.
    by JL Finney
    posted to voronoi by aengisch on 2006-12-08 07:42:10 as **
  • The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.
    J Mol Biol, Vol. 249, No. 5. (23 June 1995), pp. 955-966.
    by M Gerstein, J Tsai, M Levitt
    posted to cubic-lattice by aengisch on 2006-12-08 07:40:12 as **
  • Packing at the protein-water interface.
    Proc Natl Acad Sci U S A, Vol. 93, No. 19. (17 September 1996), pp. 10167-10172.
    by M Gerstein, C Chothia
    posted to cubic-lattice by aengisch on 2006-12-08 07:39:42 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    Protein Sci, Vol. 6, No. 7. (1 July 1997), pp. 1467-1481.
    by PJ Munson, RK Singh
    posted to multi-body by aengisch on 2006-12-07 20:26:31 as **** along with 1 person j3xucite
  • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
    J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501.
    by MJ Sippl
    posted to no-tag by aengisch on 2006-12-07 20:23:49 as *** along with 3 people and 2 groups marcius dgront mcbla BioinfoCIPF SGU-CIPF
  • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.
    J Mol Biol, Vol. 213, No. 4. (20 June 1990), pp. 859-883.
    by MJ Sippl
    posted to background by aengisch on 2006-12-07 20:22:07 as *** along with 7 people rabio bicko P2324548 apostola bpb tolot27 dgront
  • New scoring schemes for protein fold recognition based on Voronoi contacts.
    Bioinformatics, Vol. 14, No. 3. (1998), pp. 295-308.
    by R Zimmer, M Wöhler, R Thiele
    posted to no-tag by aengisch on 2006-12-07 20:18:45 as read along with 1 person siebertm
  • Statistical geometry analysis of proteins: implications for inverted structure prediction.
    Pac Symp Biocomput (1996), pp. 614-623.
    by A Tropsha, RK Singh, II Vaisman, W Zheng
    posted to four-body by aengisch on 2006-12-07 20:17:24 as read
  • 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 voronoi-overview by aengisch on 2006-12-07 20:12:16 as read along with 3 people apaydin mirzazadeh siebertm
  • A new approach to protein fold recognition based on Delaunay tessellation of protein structure.
    Pac Symp Biocomput (1997), pp. 486-497.
    by W Zheng, SJ Cho, II Vaisman, A Tropsha
    posted to four-body by aengisch on 2006-12-07 20:09:05 as **** along with 1 person j3xucite
  • Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues.
    J Comput Biol, Vol. 3, No. 2. (1996), pp. 213-221.
    by RK Singh, A Tropsha, II Vaisman
    posted to four-body by aengisch on 2006-12-07 20:08:03 as read
  • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1540-1548.
    by B Krishnamoorthy, A Tropsha
    posted to four-body by aengisch on 2006-11-27 18:17:59 as read
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