Group: Bioinformatics - with tag structure_comparison [112 articles] Export

Recent papers posted by members of the Bioinformatics group with tag structure_comparison

	Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites [My Copy] BMC Structural Biology, Vol. 8 (27 October 2008), 45. by Andrew T. Binkowski, Andrzej Joachimiak posted to protein_ligand structure_comparison by barry to the group Bioinformatics on 2009-03-25 22:12:20 as along with 2 people and 2 groups GeeSharpMinor sobolevnrm structural_bioinformatics baker-group
	Structural Alphabets for Protein Structure Classification: A Comparison Study [My Copy] Journal of Molecular Biology (25 December 2008) by Q. Le, G. Pollastri, P. Koehl posted to protein_fragments protein_structure structure_comparison by barry to the group Bioinformatics on 2009-03-12 18:15:21 as along with 4 people and 1 group zwang svozil idoerg reyez structural_bioinformatics
	Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 60, No. Pt 12 Pt 1. (01 December 2004), pp. 2256-2268. by E. Krissinel, K. Henrick posted to structure_comparison protein_structure graph bioinf_methods by barry to the group Bioinformatics on 2007-07-13 19:39:15 as along with 4 people and 3 groups parnell jwm analogAI robert structural_bioinformatics Radiation_Damage Stressosome
	SISYPHUS--structural alignments for proteins with non-trivial relationships. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (January 2007) by A. Andreeva, A. Prlić, T. J. Hubbard, A. G. Murzin posted to structure_comparison structure_classification protein_structure by ana to the group Bioinformatics on 2007-05-29 23:18:59 as along with 5 people and 1 group timhubbard barry dgront massivemayhem martainn structural_bioinformatics
	Less is more: towards an optimal universal description of protein folds. [My Copy] Bioinformatics, Vol. 21 Suppl 2 (1 September 2005) by J. D. Szustakowski, S. Kasif, Z. Weng posted to structure_comparison structure_classification protein_structure fold_space by ana to the group Bioinformatics on 2007-03-28 04:20:00 as along with 3 people and 1 group barry msierk krishnaJCSG structural_bioinformatics
	A new progressive-iterative algorithm for multiple structure alignment [My Copy] Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3255-3263. by Dmitry Lupyan, Alejandra Leo-Macias, Angel R. Ortiz posted to structure_comparison structure_alignment protein_structure by ana to the group Bioinformatics on 2007-01-16 06:07:56 as along with 3 people and 1 group dimka analogAI insectopalo structural_bioinformatics
	MUSTANG: A multiple structural alignment algorithm [My Copy] 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 structure_comparison structure_alignment protein_structure by ana to the group Bioinformatics on 2007-01-16 06:02:52 as along with 5 people and 2 groups robfsouza karbak jwm rabio Thaverkamp structural_bioinformatics Microbial-Ecology
	MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. [My Copy] Protein science : a publication of the Protein Society, Vol. 11, No. 11. (1 November 2002), pp. 2606-2621. by Angel R. Ortiz, Charlie E. Strauss, Osvaldo Olmea posted to structure_comparison structure_alignment protein_structure jcsg by ana to the group Bioinformatics on 2007-01-16 01:12:02 as along with 8 people and 1 group tomjad awarlau iakes dimka jwm analogAI sebk tjimenez structural_bioinformatics
	Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. [My Copy] Curr Opin Struct Biol (3 May 2006) by Rachel Kolodny, Donald Petrey, Barry Honig posted to fold_space protein_structure protein_universe structure_classification structure_comparison by ana to the group Bioinformatics on 2006-10-24 23:00:17 as along with 3 people and 1 group wouterboomsma dgront Inchoate structural_bioinformatics
	Bio3d: an R package for the comparative analysis of protein structures. [My Copy] Bioinformatics (29 August 2006) by Barry J J. Grant, Ana P C P. Rodrigues, Karim M M. Elsawy, J Andrew A. McCammon, Leo S D S. Caves posted to structure_superposition structure_comparison sequence_comparison r protein_structure pca multiple_structure_comparison molecular_dynamics mine by ana to the group Bioinformatics on 2006-10-11 03:38:28 as along with 9 people and 1 group dfdong dswan gisle barry Einat plofje krishnaJCSG insectopalo cdeane structural_bioinformatics
	THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures [My Copy] Bioinformatics, Vol. 22, No. 17. (1 September 2006), pp. 2171-2172. by Douglas L. Theobald, Deborah S. Wuttke posted to algorithms pca structure_comparison structure_superposition by ana to the group Bioinformatics on 2006-09-02 19:55:00 as along with 1 person and 1 group dimka structural_bioinformatics
	Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. [My Copy] Genome Res, Vol. 11, No. 10. (October 2001), pp. 1632-1640. by H. Hegyi, M. Gerstein posted to multi-domain protein_sequence protein_structure sequence_comparison structure_comparison by ana to the group Bioinformatics on 2006-06-21 22:21:00 as along with 2 people and 1 group jameswasmuth tny structural_bioinformatics
	Helix to helix packing in proteins [My Copy] Journal of Molecular Biology, Vol. 145, No. 1. (5 January 1981), pp. 215-250. by Cyrus Chothia, Michael Levitt, Douglas Richardson posted to protein_structure structure_comparison by ana to the group Bioinformatics on 2006-06-07 00:53:47 as along with 1 person and 1 group barry structural_bioinformatics
	How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins [My Copy] Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230. by Arthur M. Lesk, Cyrus Chothia posted to protein_structure sequence_structure structure_comparison structure_core structure_flexible structure_prediction by ana to the group Bioinformatics on 2006-04-27 02:08:31 as along with 2 people and 3 groups barry marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
	Significance of structural changes in proteins: expected errors in refined protein structures. [My Copy] Protein Sci, Vol. 4, No. 11. (November 1995), pp. 2392-2404. by R. M. Stroud, E. B. Fauman posted to protein_structure structure_comparison by ana to the group Bioinformatics on 2006-03-10 07:30:48 as along with 1 person and 1 group barry structural_bioinformatics
	Experimental assessment of differences between related protein crystal structures. [My Copy] Acta Crystallogr D Biol Crystallogr, Vol. 55, No. 11. (November 1999), pp. 1878-1884. by G. J. Kleywegt posted to protein_structure structure_comparison by ana to the group Bioinformatics on 2006-03-10 07:29:48 as along with 1 person and 1 group barry structural_bioinformatics
	Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. [My Copy] Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3360-3368. by J. Espadaler, O. Romero-Isart, R. M. Jackson, B. Oliva posted to protein_protein protein_sequence protein_structure sequence_comparison structure_comparison by barry to the group Bioinformatics on 2006-03-06 22:20:06 as along with 2 people and 1 group bicko baldo structural_bioinformatics
	HCPM--program for hierarchical clustering of protein models. [My Copy] Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3179-3180. by D. Gront, A. Kolinski posted to bioinf_methods protein_structure structure_comparison by barry to the group Bioinformatics on 2006-03-06 22:17:59 as along with 2 people and 1 group dgront rabio structural_bioinformatics
	Data mining the protein data bank: residue interactions. [My Copy] Proteins, Vol. 49, No. 4. (1 December 2002), pp. 510-528. by T. J. Oldfield posted to active_site algorithms data_mining protein_function protein_structure structure_comparison structure_superposition by ana to the group Bioinformatics on 2006-01-31 18:26:40 as along with 2 people and 1 group blackbart rabio structural_bioinformatics
	Evaluation of protein fold comparison servers. [My Copy] Proteins, Vol. 54, No. 2. (1 February 2004), pp. 260-270. by M. Novotny, D. Madsen, G. J. Kleywegt posted to benchmark protein_structure structure_alignment structure_comparison by ana to the group Bioinformatics on 2006-01-31 01:50:43 as along with 2 people and 3 groups reyez jwm structural_bioinformatics Radiation_Damage Stressosome
	Pairwise protein structure alignment based on an orientation-independent backbone representation. [My Copy] J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 699-717. by J. Ye, R. Janardan, S. Liu posted to bioinf_methods protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2006-01-25 03:30:29 as along with 1 group structural_bioinformatics
	Comparative molecular dynamics--similar folds and similar motions? [My Copy] Proteins, Vol. 61, No. 4. (1 December 2005), pp. 809-822. by Andrew Pang, Yalini Arinaminpathy, Mark S. Sansom, Philip C. Biggin posted to md_simulation structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-11-29 23:22:16 as along with 1 group structural_bioinformatics
	Automatic 3D Protein Structure Classification without Structural Alignment [My Copy] Journal of Computational Biology, Vol. 12, No. 9. (2005), pp. 1221-1241. by Zeyar Aung, Kian-Lee Tan posted to protein_structure structure_alignment structure_classification structure_comparison by ana to the group Bioinformatics on 2005-11-24 09:05:16 as along with 2 people and 7 groups barry shantanu structural_bioinformatics MathBio Biostatistics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
	Backbone and side chain dynamics of mutant calmodulin-Peptide complexes. [My Copy] Biochemistry, Vol. 44, No. 38. (27 September 2005), pp. 12627-12639. by T. I. Igumenova, A. L. Lee, A. J. Wand posted to protein_dynamics protein_function protein_structure structure_comparison by ana to the group Bioinformatics on 2005-10-09 04:05:20 as along with 1 person and 1 group lna structural_bioinformatics
	Structural Features can be Unconserved in Proteins with Similar Folds : An Analysis of Side-chain to Side-chain Contacts Secondary Structure and Accessibility [My Copy] Journal of Molecular Biology, Vol. 244, No. 3. (1 December 1994), pp. 332-350. by Robert B. Russell, Geoffrey J. Barton posted to contact_prediction protein_evolution protein_structure structure_comparison by ana to the group Bioinformatics on 2005-10-05 22:30:59 as along with 2 people and 1 group dfdong rabio structural_bioinformatics
	Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. [My Copy] J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196. by L. A. Mirny, E. I. Shakhnovich posted to protein_evolution protein_folding protein_function protein_structure sequence_comparison structure_comparison by ana to the group Bioinformatics on 2005-09-28 01:09:51 as along with 4 people and 3 groups dfdong barry Einat marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
	Assessing local structural perturbations in proteins. [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (13 September 2005) by Martin A. Lema, Julian Echave posted to protein_structure structure_comparison structure_flexible structure_superposition by ana to the group Bioinformatics on 2005-09-23 03:02:40 as along with 3 people and 1 group barry pansapiens Einat structural_bioinformatics
	Nh3D: a reference dataset of non-homologous protein structures. [My Copy] BMC Struct Biol, Vol. 5 (12 July 2005) by B. Thiruv, G. Quon, S. A. Saldanha, B. Steipe posted to database dataset protein_structure structure_classification structure_comparison by ana to the group Bioinformatics on 2005-09-23 02:56:54 as along with 1 person and 1 group kumar_physics structural_bioinformatics
	Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. [My Copy] Protein Sci, Vol. 3, No. 5. (May 1994), pp. 769-778. by D. Fischer, H. Wolfson, S. L. Lin, R. Nussinov posted to bioinf_methods protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-09-19 22:03:37 as along with 4 people and 1 group aalibes shadowman tjimenez chrys structural_bioinformatics
	Extracting hydrogen-bond signature patterns from protein structure data. [My Copy] Appl Bioinformatics, Vol. 3, No. 2-3. (2004), pp. 125-135. by T. Prasad, T. Subramanian, S. Hariharaputran, H. S. Chaitra, N. Chandra posted to hydrogen-bond protein_stability protein_structure structure_comparison by ana to the group Bioinformatics on 2005-09-07 20:05:22 as along with 1 group structural_bioinformatics
	Detection of hydrogen-bond signature patterns in protein families. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 167-168. by T. Prasad, M. N. Prathima, N. Chandra posted to hydrogen-bond protein_evolution protein_stability protein_structure structure_comparison web_server by ana to the group Bioinformatics on 2005-09-07 20:01:20 as along with 1 group structural_bioinformatics
	Small Libraries of Protein Fragments Model Native Protein Structures Accurately [My Copy] Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 297-307. by Rachel Kolodny, Patrice Koehl, Leonidas Guibas, Michael Levitt posted to comparative_model protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-09-07 17:59:27 as along with 1 group structural_bioinformatics
	Small libraries of protein fragments model native protein structures accurately. [My Copy] J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307. by R. Kolodny, P. Koehl, L. Guibas, M. Levitt posted to comparative_modeling protein_design protein_evolution protein_structure structure_comparison structure_fragments by ana to the group Bioinformatics on 2005-09-07 17:58:32 as along with 3 people and 1 group barry eckart_bindewald j3xucite structural_bioinformatics
	Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure [My Copy] Proteins: Structure, Function, and Genetics, Vol. 3, No. 2. (1988), pp. 71-84. by Frederic M. Richards, Craig E. Kundrot posted to ddm protein_structure structure_alignment structure_comparison by ana to the group Bioinformatics on 2005-09-06 19:46:09 as along with 1 person and 1 group Vadikus structural_bioinformatics
	Residue packing in proteins: Uniform distribution on a coarse-grained scale [My Copy] Journal of Chemical Physics, Vol. 116, No. 5. (February 2002), pp. 2269-1176. by Z. Bagci, R. L. Jernigan, Bahar posted to interaction_hierarchy protein_structure structure_comparison by ana to the group Bioinformatics on 2005-09-02 18:18:44 as along with 1 group structural_bioinformatics
	The origin and extent of coarse-grained regularities in protein internal packing. [My Copy] Proteins, Vol. 53, No. 1. (1 October 2003), pp. 56-67. by Z. Bagci, A. Kloczkowski, R. L. Jernigan, I. Bahar posted to interaction_hierarchy protein_structure structure_comparison by ana to the group Bioinformatics on 2005-09-02 18:12:43 as along with 1 person and 1 group aqeel structural_bioinformatics
	Dynamics of large proteins through hierarchical levels of coarse-grained structures. [My Copy] J Comput Chem, Vol. 23, No. 1. (15 January 2002), pp. 119-127. by P. Doruker, R. L. Jernigan, I. Bahar posted to interaction_hierarchy protein_dynamics protein_structure structure_comparison by ana to the group Bioinformatics on 2005-09-02 18:10:40 as along with 2 people and 1 group baaden aqeel structural_bioinformatics
	Molecular mechanism of domain swapping in proteins: an analysis of slower motions. [My Copy] Biophys J, Vol. 86, No. 6. (June 2004), pp. 3846-3854. by S. Kundu, R. L. Jernigan posted to protein_dynamics protein_structure structure_comparison structure_flexible by ana to the group Bioinformatics on 2005-09-02 18:09:44 as along with 1 group structural_bioinformatics
	Structural genomics: computational methods for structure analysis. [My Copy] Protein Sci, Vol. 12, No. 9. (September 2003), pp. 1813-1821. by S. Goldsmith-Fischman, B. Honig posted to protein_structure structural_genomics structure_alignment structure_comparison target_selection by ana to the group Bioinformatics on 2005-09-01 20:14:26 as along with 4 people and 1 group dfdong tjimenez vavi mijogiffin structural_bioinformatics
	Modeling conformational change in macromolecules as an elastic deformation. [My Copy] Proteins, Vol. 10, No. 2. (1991), pp. 162-170. by L. C. Andrews, R. W. Harrison posted to protein_structure structure_alignment structure_comparison structure_superposition by ana to the group Bioinformatics on 2005-08-31 19:29:37 as along with 1 person and 1 group pansapiens structural_bioinformatics
	Fragnostic: walking through protein structure space. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by I. Friedberg, A. Godzik posted to protein_function protein_structure protein_universe structure_classification structure_comparison by ana to the group Bioinformatics on 2005-08-29 20:57:23 as along with 8 people and 3 groups dfdong barry pansapiens aalibes Einat marcius alexg eweaver structural_bioinformatics BioinfoCIPF SGU-CIPF
	Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. [My Copy] Protein Sci, Vol. 13, No. 7. (July 2004), pp. 1865-1874. by V. A. Ilyin, A. Abyzov, C. M. Leslin posted to protein_universe structure_alignment structure_comparison by ana to the group Bioinformatics on 2005-08-12 21:06:56 as along with 3 people and 1 group medic0747 reyez analogAI structural_bioinformatics
	Structural mechanisms for domain movements in proteins [My Copy] Biochemistry, Vol. 33, No. 22. (1994), pp. 6739-6749. by M. Gerstein, A. Lesk, C. Chothia posted to protein_dynamics protein_structure structure_comparison structure_flexible by ana to the group Bioinformatics on 2005-08-12 20:36:38 as along with 4 people and 4 groups barry pansapiens tny joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	A geometric invariant-based framework for the analysis of protein conformational space [My Copy] Bioinformatics, Vol. Advance Access (11 August 2005) by A. V. Tendulkar, M. A. Sohoni, B. Ogunnaike, P. P. Wangikar posted to model_refinement pca protein_structure structure_comparison by ana to the group Bioinformatics on 2005-08-12 20:29:10 as along with 1 person and 1 group lsdc1 structural_bioinformatics
	A surface of minimum area metric for the structural comparison of proteins. [My Copy] J Mol Biol, Vol. 258, No. 5. (24 May 1996), pp. 871-892. by A. Falicov, F. E. Cohen posted to protein_structure structure_alignment structure_comparison structure_superposition by ana to the group Bioinformatics on 2005-06-23 21:23:16 as along with 2 people and 1 group barry baaden structural_bioinformatics
	FSSA: a novel method for identifying functional signatures from structural alignments. [My Copy] Bioinformatics (28 April 2005) by Kai Wang, Ram Samudrala posted to function_prediction protein_function protein_structure structure_comparison by ana to the group Bioinformatics on 2005-06-16 19:29:55 as along with 2 people and 1 group barry Einat structural_bioinformatics
	Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach [My Copy] Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1002-1009. by Sandelin Erik posted to multiple_structure_alignment protein_structure structure_comparison by ana to the group Bioinformatics on 2005-06-16 19:28:19 as along with 1 person and 1 group barry structural_bioinformatics
	A new progressive-iterative algorithm for multiple structure alignment. [My Copy] Bioinformatics (7 June 2005) by Dmitry Lupyan, Alejandra Leo-Macias, Angel R R. Ortiz posted to multiple_structure_alignment protein_structure structure_comparison by ana to the group Bioinformatics on 2005-06-16 19:26:37 as along with 5 people and 3 groups tomjad sebk dimka marcius tjimenez structural_bioinformatics BioinfoCIPF SGU-CIPF
	Finding an average core structure: application to the globins. [My Copy] Proc Int Conf Intell Syst Mol Biol, Vol. 2 (1994), pp. 19-27. by R. B. Altman, M. Gerstein posted to core_residues core_structure protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-06-08 18:45:13 as along with 1 group structural_bioinformatics
	Average core structures and variability measures for protein families: application to the immunoglobulins. [My Copy] J Mol Biol, Vol. 251, No. 1. (4 August 1995), pp. 161-175. by M. Gerstein, R. B. Altman posted to core_residues core_structure protein_structure structure_comparison by barry to the group Bioinformatics on 2005-06-08 01:04:23 as along with 1 group structural_bioinformatics

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protein_structure	269
structure_alignment	115
structure_classification	52
protein_evolution	42
contact_maps	32
benchmark	30
fold_space	30
structure_superposition	30
structural_bioinformatics	26
sequence_comparison	25
protein_dynamics	20
bioinf_methods	19
homology_analogy	18
sequence_structure	18
structure_flexible	18
protein_design	16
protein_function	15
protein_universe	15
flexible_structure_alignment	12
protein_sequence	12
score	12
web_server	12
structure_prediction	10
multiple_structure_alignment	9
multiple_structure_comparison	9
rmsd	9
sequence_alignment	9
core_residues	8
core_structure	8
pca	7
algorithms	6
hydrogen-bond	6
interaction_hierarchy	6
local_structure_similarity	6
protein_stability	6
review	6
structure_core	6
protein_fragments	5
comparative_model	4
mine	4
r	4
active_site	3
comparative_modeling	3
contact_map	3
contact_prediction	3
data_mining	3
database	3
dataset	3
ddm	3
delaunay	3
dynamic_programming	3
function_prediction	3
graph	3
jcsg	3
md_simulation	3
molecular_dynamics	3
multi-domain	3
multiple_sequence_alignment	3
protein_folding	3
protein_ligand	3
protein_protein	3
structural_genomics	3
structure_fragments	3
structure_invariant	3
target_selection	3
29-oct-09	2
comparison_methods	2
electrostatics	2
functional_characterisation	2
functional_residues	2
structure_determination	2
structure_similarity	2
tyrosine_phosphatases	2
citrate_synthase	1
clustering	1
contact_map_similarity	1
contacts	1
contacts_prediction	1
ctbp	1
footprinting	1
hinge_motion	1
kinesin	1
measure	1
metric	1
networks	1
nma	1
protein	1
sheer_motion	1
statistical_validation	1
structure	1
tools	1
torsion_angles	1

Group: Bioinformatics - with tag structure_comparison [112 articles] Export

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