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	FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000485. by Oliver C. Redfern, Benoît H. Dessailly, Timothy J. Dallman, Ian Sillitoe, Christine A. Orengo posted to structure_comparison functional_residues functional_characterisation comparison_methods 29-oct-09 by CorinYeats to the group Orengo Group Journal Picks on 2009-10-29 12:37:01 as along with 3 people kiekyon TRHvidsten neils
	Protein structure similarity from Principle Component Correlation analysis. [My Copy] BMC bioinformatics, Vol. 7, No. 1. (25 January 2006) by X. Zhou, J. Chou, S. T. Wong posted to structure_comparison by richardbickerton on 2009-07-30 12:39:37 as along with 1 person bicko
	Advances and pitfalls of protein structural alignment [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (27 June 2009), pp. 341-348. by Hitomi Hasegawa, Liisa Holm posted to review structural_bioinformatics structure_comparison by barry to the group structural_bioinformatics on 2009-06-08 04:25:56 as along with 5 people and 2 groups dfdong sebk davidalee dgront sobolevnrm OPIG Orengo Group Journal Picks
	Nothing about protein structure classification makes sense except in the light of evolution [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (24 June 2009), pp. 329-334. by Ruben E. Valas, Song Yang, Philip E. Bourne posted to protein_evolution protein_structure structure_comparison by barry to the group structural_bioinformatics on 2009-05-12 03:32:02 as along with 13 people and 2 groups dfdong mkotlyar skywalkerus02 dgront nyyu robfsouza apaydin coela Zephyrus sobolevnrm zwang friendpine paulschlesinger R.E.A.D baker-group
	Large-scale structural analysis of the classical human protein tyrosine phosphatome. [My Copy] Cell, Vol. 136, No. 2. (23 January 2009), pp. 352-363. by A. J. Barr, E. Ugochukwu, W. H. Lee, et al.O. N. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Müller, S. Knapp posted to electrostatics protein_structure structure_comparison tyrosine_phosphatases by barry to the group structural_bioinformatics on 2009-03-30 18:41:31 as along with 2 people absterga renatomilani
	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 structural_bioinformatics on 2009-03-25 22:12:20 as along with 2 people and 2 groups GeeSharpMinor sobolevnrm 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 structural_bioinformatics on 2009-03-12 18:15:22 as along with 4 people and 1 group zwang svozil idoerg reyez Bioinformatics
	Dictionary of recurrent domains in protein structures [My Copy] 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. [My Copy] BMC Bioinformatics, Vol. 7 (April 2006), 206. by V. Sam, C. H. Tai, J. Garnier, J. F. Gibrat, B. Lee, P. J. Munson posted to structure_comparison by rabio on 2008-04-14 19:41:51 as along with 1 person karbak
	DaliLite workbench for protein structure comparison. [My Copy] Bioinformatics (Oxford, England), 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 4 people jwm tomjad semin sim82
	Comment on 'Using quaternions to calculate RMSD' [J. Comp. Chem. 25, 1849 (2004)] [My Copy] Journal of Computational Chemistry, Vol. 26 (June 2005), pp. 1660-1662. by G. R. 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 [My Copy] 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 [My Copy] 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 6 people eskay Diego_Prada BragilMassoud apaydin nachtalp dgront
	Rotational superposition: a review of methods [My Copy] 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
	A note on the rotational superposition problem [My Copy] 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 [My Copy] 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
	Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures [My Copy] 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 along with 5 people mijam nickolay blackbart choonpeng higueruelo
	A solution for the best rotation to relate two sets of vectors [My Copy] 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 along with 3 people reyez pavanghatty gisle
	A discussion of the solution for the best rotation to relate two sets of vectors [My Copy] 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 along with 1 person gisle
	Comparative Analysis of Protein Structure Alignments [My Copy] BMC Structural Biology, Vol. 7 (26 July 2007), 50. by Gabriele Mayr, Francisco S. Domingues, Peter Lackner posted to protein_structure review structure_comparison by barry to the group structural_bioinformatics on 2007-12-04 22:41:13 as along with 1 person bicko
	Algorithmic aspects of protein structure similarity [My Copy] Foundations of Computer Science, 1999. 40th Annual Symposium on In Foundations of Computer Science, 1999. 40th Annual Symposium on (1999), pp. 512-521. by D. Goldman, S. Istrail, C. Papadimitriou posted to contact_maps structure_alignment structure_comparison by rabio on 2007-07-19 13:17:40 as along with 2 people and 2 groups ana vavi structural_bioinformatics 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 contacts_prediction structure_comparison by rabio on 2007-07-19 12:51:23 as along with 2 people and 2 groups dfdong ana structural_bioinformatics 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 bioinf_methods graph protein_structure structure_comparison by barry on 2007-07-13 19:39:15 as along with 4 people and 4 groups parnell jwm analogAI robert structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
	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 protein_fragments protein_structure structure_comparison by barry on 2007-05-30 19:09:40 as along with 5 people and 2 groups timhubbard ana dgront massivemayhem martainn structural_bioinformatics 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 fold_space protein_structure structure_classification structure_comparison by ana on 2007-03-28 04:20:00 as along with 3 people and 2 groups barry msierk krishnaJCSG structural_bioinformatics Bioinformatics
	Statistical validation of the root-mean-square-distance, a measure of protein structural proximity [My Copy] Protein Engineering, Design and Selection, Vol. 20, No. 1. (1 January 2007), pp. 33-37. by Oliviero Carugo posted to statistical_validation structure_comparison structure_similarity by rabio on 2007-02-12 14:46:21 as
	Measuring the similarity of protein structures by means of the universal similarity metric [My Copy] Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1015-1021. by N. Krasnogor, D. A. Pelta posted to measure metric structure_comparison structure_similarity by rabio on 2007-02-12 13:35:35 as along with 4 people and 2 groups ana okarsligil vavi rsantana structural_bioinformatics Bioinformatics
	Protein structure alignment by incremental combinatorial extension (CE) of the optimal path [My Copy] Protein Engineering, Vol. 11, No. 9. (September 1998), pp. 739-747. by I. N. Shindyalov, P. E. Bourne posted to tools structure_alignment structure_comparison by rabio on 2007-02-05 22:27:17 as along with 11 people and 2 groups medic0747 sebk reyez pjcite nigham jwm analogAI dgront siebertm Inchoate sim82 Radiation_Damage Stressosome
	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 on 2007-01-16 06:07:56 as along with 3 people and 2 groups dimka analogAI insectopalo structural_bioinformatics 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
	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 kinesin mine protein_dynamics protein_sequence protein_structure r structural_bioinformatics structure_comparison by barry on 2007-01-05 01:03:37 as along with 9 people and 2 groups dfdong dswan gisle ana Einat plofje krishnaJCSG insectopalo cdeane structural_bioinformatics 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 clustering structure_comparison by rabio on 2006-12-01 11:49:51 as along with 2 people and 2 groups barry dgront structural_bioinformatics 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
	Protein Structure Comparison Using Bipartite Graph Matching and Its Application to Protein Structure Classification [My Copy] Mol Cell Proteomics, Vol. 1, No. 4. (1 April 2002), pp. 334-339. by William R. Taylor posted to structure_classification structure_comparison by gbart on 2006-10-11 11:21:15 as along with 1 person dfdong
	Mechanisms of domain closure in proteins. [My Copy] J Mol Biol, Vol. 174, No. 1. (25 March 1984), pp. 175-191. by A. M. Lesk, C. Chothia posted to citrate_synthase ctbp hinge_motion protein_dynamics protein_structure sheer_motion structure_comparison torsion_angles by barry on 2006-09-29 19:31:06 as along with 1 person and 2 groups ana structural_bioinformatics 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 structure_determination by barry on 2006-09-29 19:23:13 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	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_sequence structure_comparison by barry on 2006-09-29 19:21:38 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Experimental assessment of differences between related protein crystal structures [My Copy] Acta Crystallographica. Section D, Biological Crystallography, Vol. 55, No. 11. (November 1999), pp. 1878-1884. by G. J. Kleywegt posted to protein_structure structure_comparison structure_determination by barry on 2006-09-29 19:20:46 as along with 1 person and 2 groups ana structural_bioinformatics 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 core_residues core_structure protein_design protein_evolution protein_sequence protein_structure sequence_comparison structure_comparison by barry on 2006-09-29 19:18:54 as along with 2 people and 4 groups ana marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. [My Copy] Proteins, Vol. 54, No. 1. (1 January 2004), pp. 71-87. by J. O. Wrabl, N. V. Grishin posted to protein_sequence protein_structure sequence_comparison structure_comparison by barry on 2006-09-29 19:17:05 as along with 4 people and 2 groups j3xucite ana analogAI granujilla structural_bioinformatics 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 structural_bioinformatics on 2006-09-02 19:55:00 as along with 1 person and 1 group dimka Bioinformatics
	LGA: A method for finding 3D similarities in protein structures. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3370-3374. by A. Zemla posted to contact_map protein structure_comparison by vavi on 2006-08-13 14:28:27 as along with 4 people and 2 groups dfdong karbak ana analogAI structural_bioinformatics Bioinformatics
	1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. [My Copy] J Comput Biol, Vol. 11, No. 1. (2004), pp. 27-52. by A. Caprara, R. Carr, S. Istrail, G. Lancia, B. Walenz posted to contact_map contact_map_similarity structure_comparison by vavi on 2006-06-27 17:06:09 as along with 2 people and 2 groups ana carlk structural_bioinformatics Bioinformatics
	Reconstruction of protein structures from a vectorial representation. [My Copy] Phys Rev Lett, Vol. 92, No. 21. (28 May 2004) by M. Porto, U. Bastolla, H. E. Roman, M. Vendruscolo posted to contact_map structure_comparison structure_prediction by vavi on 2006-06-27 15:48:24 as along with 1 person dgront
	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
	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 structural_bioinformatics on 2006-03-06 22:20:06 as along with 2 people and 1 group bicko baldo 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 bioinf_methods protein_structure structural_bioinformatics structure_comparison by barry on 2006-03-06 22:05:43 as along with 2 people and 2 groups ana Einat structural_bioinformatics 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 structural_bioinformatics on 2006-01-31 18:26:40 as along with 2 people and 1 group blackbart rabio 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

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