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tjimenez library [219 articles]

Статьи, недавно добавленные в библиотеку tjimenez .
  • Generalized solvent boundary potential for computer simulations
    Journal of chemical physics, Vol. 114, No. 7. (15 February 2001), pp. 2924-2937.
    by W Im, S Berneche, B Roux
    posted to shape harmonics by tjimenez on 2008-05-09 10:45:06 as **
  • Ultrafast shape recognition to search compound databases for similar molecular shapes.
    J Comput Chem (6 March 2007)
    by Pedro J J Ballester, W Graham G Richards
    posted to shape by tjimenez on 2008-05-09 09:29:49 as ** along with 4 people kintoki operon massivemayhem ssgong
  • SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces.
    Journal of molecular modeling, Vol. 14, No. 5. (May 2008), pp. 393-401.
    by W Cai, J Xu, X Shao, V Leroux, A Beautrait, B Maigret
    posted to harmonics by tjimenez on 2008-05-07 18:37:45 as **
  • Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening.
    Journal of molecular graphics & modelling, Vol. 20, No. 4. (January 2002), pp. 313-328.
    by W Cai, X Shao, B Maigret
    posted to harmonics by tjimenez on 2008-05-07 18:36:05 as **
  • An evaluation of spherical designs for molecular-like surfaces.
    Journal of molecular graphics & modelling, Vol. 24, No. 5. (March 2006), pp. 356-361.
    by RJ Morris
    posted to harmonics by tjimenez on 2008-05-07 18:34:57 as **
  • An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties.
    Journal of chemical information and modeling, Vol. 45, No. 4. (g 2005), pp. 1010-1016.
    by JH Lin, T Clark
    posted to harmonics by tjimenez on 2008-05-07 18:32:09 as **
  • Molecular shape and electrostatics in the encoding of relevant chemical information.
    Journal of computer-aided molecular design, Vol. 19, No. 9-10. (t 2005), pp. 661-686.
    by A Nicholls, JA Grant
    posted to shape comparison by tjimenez on 2008-05-07 18:30:21 as **
  • A Fast Method of Molecular Shape Comparison: A Simple Application of a Gaussian Description of Molecular Shape.
    Journal of computational chemistry, Vol. 17, No. 14. (1996), pp. 1653-1666.
    by JA Grant, MA Gallardo, BT Pickup
    posted to shape comparison by tjimenez on 2008-05-07 18:27:31 as **
  • Toward high throughput 3D virtual screening using spherical harmonic surface representations.
    Journal of chemical information and modeling, Vol. 47, No. 5. (t 2007), pp. 1787-1796.
    by L Mavridis, BD Hudson, DW Ritchie
    posted to harmonics by tjimenez on 2008-05-07 17:50:25 as **
  • Shape Variation in Protein Binding Pockets and their Ligands.
    J Mol Biol, Vol. 368, No. 1. (20 April 2007), pp. 283-301.
    by A Kahraman, RJ Morris, RA Laskowski, JM Thornton
    posted to harmonics by tjimenez on 2008-05-07 17:48:41 as ** along with 3 people jwm martainn grottenolm
  • An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison.
    Journal of molecular graphics & modelling, Vol. 26, No. 7. (April 2008), pp. 1035-1045.
    by L Mak, S Grandison, RJ Morris
    posted to harmonics by tjimenez on 2008-05-07 11:38:53 as **
  • Rotation invariant spherical harmonic representation of 3D shape descriptors
    (2003)
    by M Kazhdan, T Funkhouser, S Rusinkiewicz
    posted to harmonics by tjimenez on 2008-05-07 11:14:38 as **
  • Moment invariants as shape recognition technique for comparing protein binding sites
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3139-3146.
    by Ingolf Sommer, Oliver Muller, Francisco S Domingues, Oliver Sander, Joachim Weickert, Thomas Lengauer
    posted to shape by tjimenez on 2008-05-05 18:58:43 as ** along with 3 people chad_davis nickolay carlescorbi
  • Efficient shape descriptors for feature extraction in 3D protein structures.
    In silico biology, Vol. 7, No. 2. (2007), pp. 169-174.
    by A Ranganath, KC Shet, N Vidyavathi
    posted to shape by tjimenez on 2008-05-05 18:55:22 as **
  • Virtual screening in drug discovery -- a computational perspective.
    Current protein & peptide science, Vol. 8, No. 4. (August 2007), pp. 329-351.
    by AS Reddy, SP Pati, PP Kumar, HN Pradeep, GN Sastry
    posted to structure_to_function by tjimenez on 2008-05-05 18:51:17 as **
  • Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches.
    Drug discovery today, Vol. 12, No. 5-6. (March 2007), pp. 225-233.
    by H Eckert, J Bajorath
    posted to molecular_comparison by tjimenez on 2008-05-05 18:47:00 as **
  • Shape Signatures: speeding up computer aided drug discovery
    Drug Discovery Today, Vol. 11, No. 19-20. (October 2006), pp. 895-904.
    by Peter J Meek, Zhiwei Liu, Lifeng Tian, Ching Y Wang, William J Welsh, Randy J Zauhar
    posted to shape by tjimenez on 2008-05-05 18:45:14 as ** along with 1 person sithmein
  • Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.
    J Med Chem, Vol. 50, No. 6. (22 March 2007), pp. 1231-1240.
    by MR Landon, DR Lancia, J Yu, SC Thiel, S Vajda
    posted to binding_pocket_recognition by tjimenez on 2008-04-23 09:44:24 as ** along with 1 person willpitt
  • Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model.
    J Chem Inf Model, Vol. 46, No. 6. (27 November 2006), pp. 2631-2637.
    by Ryan G Coleman, Anna C Salzberg, Alan C Cheng
    posted to binding_pocket_recognition by tjimenez on 2008-04-23 09:42:24 as ** along with 2 people and 1 group caporaso cjeans biomedical-nlp
  • Utilising structural knowledge in drug design strategies: applications using Relibase.
    Journal of molecular biology, Vol. 326, No. 2. (14 February 2003), pp. 621-636.
    by J Günther, A Bergner, M Hendlich, G Klebe
    posted to binding_pocket_recognition by tjimenez on 2008-04-23 09:11:17 as **
  • Finding functional sites in structural genomics proteins.
    Structure (London, England : 1993), Vol. 12, No. 8. (August 2004), pp. 1405-1412.
    by A Stark, A Shkumatov, RB Russell
    posted to sequence_similarity binding_pocket_recognition by tjimenez on 2008-04-23 07:33:35 as **
  • Using a neural network and spatial clustering to predict the location of active sites in enzymes.
    J Mol Biol, Vol. 330, No. 4. (18 July 2003), pp. 719-734.
    by A Gutteridge, GJ Bartlett, JM Thornton
    posted to structure_to_function binding_pocket_recognition by tjimenez on 2008-04-23 07:33:03 as ** along with 6 people and 1 group chrn Einat alexg gbart eweaver sriram_s structural_bioinformatics
  • POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids.
    J Mol Graph, Vol. 10, No. 4. (December 1992), pp. 229-234.
    by DG Levitt, LJ Banaszak
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 19:32:19 as ** along with 2 people nickolay sriram_s
  • Using structural motif descriptors for sequence-based binding site prediction.
    BMC Bioinformatics, Vol. 8 Suppl 4 (2007)
    by A Henschel, C Winter, WK Kim, M Schroeder
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 11:28:20 as ** along with 1 person Evangelia
  • A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
    BMC Bioinformatics, Vol. 8 Suppl 4 (2007)
    by L Xie, PE Bourne
    posted to shape binding_pocket_recognition by tjimenez on 2008-04-22 11:27:18 as ** along with 1 person higueruelo
  • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions.
    J Mol Graph, Vol. 13, No. 5. (October 1995)
    by RA Laskowski
    posted to no-tag by tjimenez on 2008-04-22 09:28:22 as ** along with 1 person sriram_s
  • Localization of protein-binding sites within families of proteins.
    Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360.
    by D Korkin, FP Davis, A Sali
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:12:26 as ** along with 5 people and 4 groups wilbur barry bicko chad_davis marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Ligand binding: functional site location, similarity and docking.
    Curr Opin Struct Biol, Vol. 13, No. 3. (June 2003), pp. 389-395.
    by SJ Campbell, ND Gold, RM Jackson, DR Westhead
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:09:27 as ** along with 1 person blackbart
  • Fast prediction and visualization of protein binding pockets with PASS.
    J Comput Aided Mol Des, Vol. 14, No. 4. (May 2000), pp. 383-401.
    by GP Brady, PF Stouten
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:08:26 as ** along with 1 person nickolay
  • Empirical rules facilitate the search for binding sites on protein surfaces.
    Journal of molecular graphics & modelling, Vol. 25, No. 5. (January 2007), pp. 671-679.
    by H te Heesen, AM Schlitter, J Schlitter
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:06:57 as **
  • Localization of binding sites in protein structures by optimization of a composite scoring function.
    Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2366-2380.
    by A Rossi, MA Marti-Renom, A Sali
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:06:11 as ** along with 2 people nickolay MaggieYe
  • Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites.
    Proteins, Vol. 68, No. 2. (1 August 2007), pp. 516-529.
    by T Kawabata, N Go
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:05:01 as **
  • PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins.
    Journal of structural biology, Vol. 161, No. 1. (January 2008), pp. 31-42.
    by Y Kalidas, N Chandra
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:04:21 as **
  • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
    J Med Chem, Vol. 28, No. 7. (July 1985), pp. 849-857.
    by PJ Goodford
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:00:59 as ** along with 3 people papatonyhill sim82 GermanErlenkamp
  • A method for localizing ligand binding pockets in protein structures.
    Proteins, Vol. 62, No. 2. (1 February 2006), pp. 479-488.
    by F Glaser, RJ Morris, RJ Najmanovich, RA Laskowski, JM Thornton
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 09:00:03 as ** along with 4 people jwm nickolay sriram_s bilab
  • Detection, delineation, measurement and display of cavities in macromolecular structures.
    Acta Crystallogr D Biol Crystallogr, Vol. 50, No. Pt 2. (1 March 1994), pp. 178-185.
    by GJ Kleywegt, TA Jones
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:55:27 as ** along with 1 person and 2 groups jwm Radiation_Damage Stressosome
  • Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design.
    Protein Sci, Vol. 7, No. 9. (September 1998), pp. 1884-1897.
    by J Liang, H Edelsbrunner, C Woodward
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:49:50 as ** along with 2 people higueruelo nickolay
  • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.
    J Mol Biol, Vol. 256, No. 1. (16 February 1996), pp. 201-213.
    by KP Peters, J Fauck, C Frömmel
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:48:23 as ** along with 2 people nickolay sriram_s
  • Protein clefts in molecular recognition and function.
    Protein Sci, Vol. 5, No. 12. (December 1996), pp. 2438-2452.
    by RA Laskowski, NM Luscombe, MB Swindells, JM Thornton
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:47:29 as ** along with 1 person sriram_s
  • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.
    J Mol Graph Model, Vol. 15, No. 6. (December 1997)
    by M Hendlich, F Rippmann, G Barnickel
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:39:06 as ** along with 1 person nickolay
  • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    BMC Structural Biology, Vol. 6 (24 September 2006), 19.
    by Bingding Huang, Michael Schroeder
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:37:37 as ** along with 1 person nickolay
  • PocketPicker: analysis of ligand binding-sites with shape descriptors.
    Chemistry Central journal, Vol. 1 (2007)
    by M Weisel, E Proschak, G Schneider
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:37:13 as **
  • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites.
    Proteins (13 February 2006)
    by Murad Nayal, Barry Honig
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 08:36:48 as ** along with 4 people and 1 group BragilMassoud pansapiens Einat nickolay structural_bioinformatics
  • Automated prediction of ligand-binding sites in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Rodney Harris, Arthur J Olson, David S Goodsell
    posted to binding_pocket_recognition by tjimenez on 2008-04-22 07:46:52 as ** along with 2 people carlescorbi RamuAnandakrishnan
  • Functional annotation by sequence-weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.
    Proteins (2 April 2008)
    by Daron M M Standley, Hiroyuki Toh, Haruki Nakamura
    posted to structure_to_function by tjimenez on 2008-04-17 10:19:15 as **
  • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Ryoichi Minai, Yo Matsuo, Hiroyuki Onuki, Hiroshi Hirota
    posted to binding comparison sites by tjimenez on 2008-04-17 10:14:36 as ** along with 4 people higueruelo chad_davis massivemayhem mingzhi
  • ConFunc--functional annotation in the twilight zone.
    Bioinformatics (Oxford, England), Vol. 24, No. 6. (15 March 2008), pp. 798-806.
    by MN Wass, MJ Sternberg
    posted to function sequence to by tjimenez on 2008-04-17 09:50:10 as ** along with 1 person jyuh
  • A simple and fuzzy method to align and compare druggable ligand-binding sites
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger, Didier Rognan
    posted to binding comparison sites by tjimenez on 2008-04-17 09:46:45 as ** along with 2 people bicko willpitt
  • Predicting gene ontology functions from protein's regional surface structures
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Zhi P Liu, Ling Y Wu, Yong Wang, Luonan Chen, Xiang S Zhang
    posted to structure_to_function by tjimenez on 2008-04-17 09:38:53 as ** along with 2 people carlk neils
  • Comparisons of protein family dynamics.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 426-437.
    by AJ Rader, JT Harrell
    posted to classification family by tjimenez on 2008-04-17 09:37:15 as **
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