Tag pdb [102 articles] Export

Recent papers classified by the tag pdb.

	3D-footprint: a database for the structural analysis of protein-DNA complexes [My Copy] Nucl. Acids Res. (18 September 2009), gkp781. by Bruno Contreras-Moreira posted to protein pdb footprint dna database by brunocontreras on 2009-11-08 21:39:08 as
	PDBe: Protein Data Bank in Europe [My Copy] Nucl. Acids Res. (25 October 2009), gkp916. by S. Velankar, C. Best, B. Beuth, et al.C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. J. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. Swaminathan, G. van Ginkel, W. F. Vranken, K. Henrick, G. J. Kleywegt posted to wwpdb protein_structure pdbe pdb ebi database by walshtp on 2009-11-04 15:26:46 as
	The Protein Data Bank [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 235-242. by Helen M. Berman, John Westbrook, Zukang Feng, et al.Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne posted to pdb by viktor21614 on 2009-10-09 10:25:53 as along with 43 people and 5 groups barmak7282 badi ucbcjbm TLVincent maria_hauser Martin8223 tomjad Diego_Prada flbarroso Taguan oceanwind dsmueller fisherp semin MarcoAlvarez kumar_physics LamBras RamuAnandakrishnan nlapalu reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon aengisch debatebob massivemayhem gisle girschick selrac tji higueruelo boris_aguilar sebk timg References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp beta
	The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries [My Copy] Journal of Biomolecular NMR by Jurgen Doreleijers, Wim Vranken, Christopher Schulte, et al.Jundong Lin, Jonathan Wedell, Christopher Penkett, Geerten Vuister, Gert Vriend, John Markley, Eldon Ulrich posted to pdb_entries pdb nmr bmrb by viktor21614 on 2009-10-09 09:51:35 as along with 1 person apaydin
	3D structure of Alzheimer's amyloid-Î²(1â42) fibrils [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 48. (29 November 2005), pp. 17342-17347. by Thorsten LÃ¼hrs, Christiane Ritter, Marc Adrian, et al.Dominique Riek-Loher, Bernd Bohrmann, Heinz DÃ¶beli, David Schubert, Roland Riek posted to pdb exp amyloid by ashaytan3 on 2009-10-05 07:11:47 as along with 3 people aip chiufanlee cactus
	Probability Distributions of Hydration Water Molecules around Polar Protein Atoms Obtained by a Database Analysis [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 32. (13 August 2009), pp. 11274-11292. by Daisuke Matsuoka, Masayoshi Nakasako posted to water_slaving protein pdb hydration by whitead to the group Jiang Research Group on 2009-10-01 18:13:12 as
	The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value [My Copy] Comput. Appl. Biosci., Vol. 12, No. 6. (1 December 1996), pp. 525-529. by R. W. W. Hooft, C. Sander, M. Scharf, G. Vriend posted to structure protein pdb assignment by TLVincent on 2009-09-17 15:41:51 as
	Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 1. (1 January 2008), pp. 1-24. by Ken A. Brameld, Bernd Kuhn, Deborah C. Reuter, Martin Stahl posted to smallmol pdb conformation ccdc by dimka on 2009-08-20 18:19:49 as along with 2 people pslee daevans
	Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000470. by Mati Cohen, Vladimir Potapov, Gideon Schreiber posted to structure protein pdb amino acids by ericrpaquet on 2009-08-14 14:41:11 as along with 6 people nickolay klexa Diego_Prada zwang reyez TRHvidsten
	Structure of the cross-[beta] spine of amyloid-like fibrils [My Copy] Nature, Vol. 435, No. 7043. (9 June 2005), pp. 773-778. by Rebecca Nelson, Michael R. Sawaya, Melinda Balbirnie, et al.Anders O. Madsen, Christian Riekel, Robert Grothe, David Eisenberg posted to peptides pdb exp amyloid by ashaytan3 on 2009-08-12 08:11:54 as along with 2 people pjkiley cactus
	LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (January 2008) by Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak posted to binding bound database pdb protein structure unbound by bdessailly to the group Orengo Group Journal Picks on 2009-08-03 04:25:06 as along with 1 person ramensky
	PDBML: the representation of archival macromolecular structure data in XML [My Copy] Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 988-992. by John Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman posted to pdb pdbml xml by walshtp on 2009-07-29 13:13:55 as along with 3 people and 1 group neils sobolevnrm chad_davis baker-group
	The PDB format, mmCIF, and other data formats. [My Copy] Methods of biochemical analysis, Vol. 44 (2003), pp. 161-179. by J. D. Westbrook, P. M. Fitzgerald posted to mmcif pdb protein-structure standards structure by idoerg on 2009-07-07 20:54:17 as
	PDB file parser and structure class implemented in Python [My Copy] Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2308-2310. by Thomas Hamelryck, Bernard Manderick posted to 2003 biopython parser pdb structure by klexa on 2009-06-29 15:29:34 as along with 7 people and 1 group edws oteri dgruiz bicko dgront rabio massivemayhem Structural Biology Group TorVergata
	The Membrane Protein Data Bank. [My Copy] Cellular and molecular life sciences : CMLS, Vol. 63, No. 1. (January 2006), pp. 36-51. by P. Raman, V. Cherezov, M. Caffrey posted to pdb by leocmcheung on 2009-06-09 15:36:15 as along with 1 person and 1 group guhjy MuraLab
	The RCSB PDB information portal for structural genomics. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006) by A. Kouranov, L. Xie, de La, et al.L. Chen, J. Westbrook, P. E. Bourne, H. M. Berman posted to pdb by kumar_physics on 2009-06-05 12:43:03 as along with 2 people and 2 groups mgomes marcius BioinfoCIPF SGU-CIPF
	The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_1. (1 January 2005), pp. D233-237. by Nita Deshpande, Kenneth J. Addess, Wolfgang F. Bluhm, et al.Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel K. Green, Judith L. Flippen-Anderson, John Westbrook, Helen M. Berman, Philip E. Bourne posted to pdb by kumar_physics on 2009-06-05 12:42:43 as along with 1 person flbarroso
	The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D301-D303. by Berman, Helen, Henrick, et al. Kim, Nakamura, Haruki, Markley, L. John posted to pdb by kumar_physics on 2009-06-05 12:40:45 as
	Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. [My Copy] The Journal of biological chemistry, Vol. 269, No. 42. (21 October 1994), pp. 26344-26348. by Z. Chen, Y. Li, E. Chen, et al.D. L. Hall, P. L. Darke, C. Culberson, J. A. Shafer, L. C. Kuo posted to pdb by tovrstra on 2009-05-24 16:49:34 as along with 1 person lalgarve
	VMD: Visual molecular dynamics [My Copy] Journal of Molecular Graphics, Vol. 14, No. 1. (February 1996), pp. 33-38. by W. Humphrey posted to ache amber amyloid beta-propeller binary binarytrehalose desmond ethanol gaff glycerol hsa hydrationwater hydrogenbond icenano iqt letter lysozyme massspec mdintro ornl pdb reading research_intro residence_times rotationaldiff slaving structure_function swell td ten_rules tip3p tobias trehalose water by pavanghatty on 2009-04-26 01:52:09 as along with 6 people and 1 group whitead csrocha r2s2 choonpeng RamuAnandakrishnan tji Jiang Research Group
	LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures [My Copy] Bioinformatics (15 April 2009), btp242. by Michael Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin posted to pdb snps visualization by Cortel on 2009-04-16 17:53:02 as along with 1 person guhjy
	Structure of phosphate-free ribonuclease A refined at 1.26 A. [My Copy] Biochemistry, Vol. 27, No. 8. (19 April 1988), pp. 2705-2717. by A. Wlodawer, L. A. Svensson, L. Sjölin, G. L. Gilliland posted to glycerol pdb by pavanghatty on 2009-04-04 16:14:41 as
	MMDB: annotating protein sequences with Entrez's 3D-structure database [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D298-D300. by Wang, Yanli, Addess, et al.J. Kenneth, Chen, Jie, Geer, Y. Lewis, He, Jane, He, Siqian, Lu, Shennan, Madej, Thomas, Marchler-Bauer, Aron, Thiessen, A. Paul, Zhang, Naigong, Bryant, H. Stephen posted to mapping mmdb pdb sequence structure uniprot by ssgong on 2009-03-05 22:48:42 as along with 1 person dsmueller
	The IMB Jena Image Library of Biological Macromolecules: 2002 update [My Copy] Nucl. Acids Res., Vol. 30, No. 1. (1 January 2002), pp. 253-254. by Jan Reichert, Jurgen Suhnel posted to jenalib mapping pdb sequence structure uniprot by ssgong on 2009-03-05 22:36:36 as along with 1 person reyez
	PDBsum new things. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (1 January 2009), pp. D355-359. by R. A. Laskowski posted to mapping pdb pdbsum sequence structure uniprot by ssgong on 2009-03-05 22:20:35 as along with 3 people grottenolm bicko lptolik
	SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase [My Copy] BMC Bioinformatics, Vol. 9 (23 September 2008), 391. by Fabrice P. A. David, Yum L. Yip posted to mapping pdb sequence structure uniprot by ssgong on 2009-03-05 21:57:03 as along with 1 person niallhaslam
	Seq2Struct: a resource for establishing sequence-structure links [My Copy] Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 551-553. by Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich posted to mapping pdb sequence structure to uniprot by ssgong on 2009-03-05 21:56:18 as
	Mapping PDB chains to UniProtKB entries [My Copy] Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4297-4301. by Andrew C. Martin posted to mapping pdb sequence structure to uniprot by ssgong on 2009-03-05 21:46:41 as
	Solution structure of the cysteine-rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 3. (March 2009), pp. 650-656. by Fahu He, Weirong Dang, Kohei Saito, et al.Satoru Watanabe, Naohiro Kobayashi, Peter Güntert, Takanori Kigawa, Akiko Tanaka, Yutaka Muto, Shigeyuki Yokoyama posted to 2rpj p3000 pdb by Takao on 2009-03-04 02:09:53 as along with 1 person tprpip
	Announcing the worldwide Protein Data Bank [My Copy] Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980. by Helen Berman, Kim Henrick, Haruki Nakamura posted to pdb by kumar_physics on 2009-02-12 12:12:16 as along with 5 people hadesnumb gjuggler massivemayhem allmensch reyez
	3did Update: domain-domain and peptide-mediated interactions of known 3D structure. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (25 January 2009), gkn690. by Amelie Stein, Alejandro Panjkovich, Patrick Aloy posted to 2008 3did db pdb ppi by higueruelo on 2009-02-10 15:12:06 as along with 4 people lptolik zdai neils barriot
	CREDO: A Protein-Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to 2009 credo pdb sm-prot by higueruelo on 2009-01-26 17:32:33 as along with 6 people mijam richardbickerton pansapiens bicko nanonan massivemayhem
	The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery [My Copy] J. Med. Chem. (1 November 2008) by Johannes Kirchmair, Patrick Markt, Simona Distinto, et al.Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Thierry Langer, Gerhard Wolber posted to database pdb protein review structure by nickolay on 2009-01-13 18:59:57 as along with 2 people guhjy reyez
	Protein structure databases with new web services for structural biology and biomedical research. [My Copy] Briefings in bioinformatics, Vol. 9, No. 4. (22 July 2008), pp. 276-285. by Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura posted to pdb rest web_service by Cortel on 2009-01-11 02:16:28 as along with 5 people tprpip flbarroso guhjy dullhunk reyez
	The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8. [My Copy] Journal of molecular biology, Vol. 384, No. 4. (26 December 2008), pp. 954-966. by G. Benison, P. A. Karplus, E. Barbar posted to 3bri 3e2b als dynein pdb by zfekete to the group HEIRS ALS on 2008-12-04 11:37:31 as
	Realism about PDB [My Copy] Nature Biotechnology, Vol. 25, No. 8., pp. 845-846. by Helen M. Berman, Kim Henrick, Haruki Nakamura, John Markley, Philip E. Bourne, John Westbrook posted to pdb by dullhunk on 2008-12-02 15:44:07 as along with 2 people hpiwowar reyez
	Overhauling the PDB. [My Copy] Nature biotechnology, Vol. 25, No. 4. (April 2007), pp. 437-442. by Amanda C. Schierz, Larisa N. Soldatova, Ross D. King posted to larisa-soldatova mmcif pdb ross-king database by dullhunk on 2008-12-02 15:12:24 as along with 4 people daforerog jerome viktor21614 bicko
	MolTalk--a programming library for protein structures and structure analysis. [My Copy] BMC Bioinformatics, Vol. 5 (19 April 2004) by A. V. Diemand, H. Scheib posted to pdb programming structure by mijogiffin on 2008-11-10 05:58:31 as along with 1 person bicko
	PiSite: a database of protein interaction sites using multiple binding states in the PDB [My Copy] Nucl. Acids Res. (4 October 2008), gkn659. by Miho Higurashi, Takashi Ishida, Kengo Kinoshita posted to binding database interaction pdb protein-protein sites by neils on 2008-10-05 10:09:38 as along with 3 people semin robfsouza kintoki
	Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 4. (1 February 2007), pp. 726-741. by Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari, et al.Suzanne C. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray posted to docking pdb by massivemayhem on 2008-09-25 12:02:39 as along with 9 people flbarroso GermanErlenkamp higueruelo BragilMassoud daevans ramensky hmk superpyrin thanatos
	Mapping PDB chains to UniProtKB entries. [My Copy] Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4297-4301. by A. C. Martin posted to mapping pdb uniprot by saunders on 2008-07-24 10:51:12 as along with 3 people bicko grahamc lpfernandes
	Interferometric CO Observations of submillimeter-faint, radio-selected starburst galaxies at z~2 [My Copy] (23 Jul 2008) by S. C. Chapman, R. Neri, F. Bertoldi, et al.Ian Smail, T. R. Greve, D. Trethewey, A. W. Blain, P. Cox, R. Genzel, R. J. Ivison, A. Kovacs, Omont posted to high-z pdb submm by bnikolic on 2008-07-24 07:15:37 as along with 1 person mojin
	Transmembrane proteins in the Protein Data Bank: identification and classification. [My Copy] Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 2964-2972. by G. E. Tusnády, Z. Dosztányi, I. Simon posted to membrane_protein pdb by viktor21614 on 2008-07-22 15:33:11 as along with 4 people and 1 group kallberg chrn xdeupi sebk LabCompMed
	The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. [My Copy] Nucleic Acids Research, Vol. 35, No. Database issue. (January 2007), pp. D301-D303. by H. Berman, K. Henrick, H. Nakamura, J. L. Markley posted to pdb wwpdb by reyez on 2008-07-18 10:27:18 as along with 2 people mgomes bicko
	Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. [My Copy] Biochemistry, Vol. 32, No. 42. (26 October 1993), pp. 11259-11269. by S. E. Jackson, M. Moracci, N. elMasry, C. M. Johnson, A. R. Fersht posted to 1coa pdb thesis by nigham on 2008-07-17 07:09:55 as
	A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742. by N. D. Gold, R. M. Jackson posted to binding geometric hashing pdb sites by reyez on 2008-07-16 09:29:52 as along with 4 people and 1 group medic0747 caporaso blackbart massivemayhem biomedical-nlp
	The CATH database: an extended protein family resource for structural and functional genomics. [My Copy] Nucleic acids research, Vol. 31, No. 1. (1 January 2003), pp. 452-455. by F. M. Pearl, C. F. Bennett, J. E. Bray, et al.A. P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, C. A. Orengo posted to cath families pdb structural by nigham on 2008-07-02 13:34:59 as along with 3 people and 1 group sillitoe flbarroso yuslinaz Orengo Group Journal Picks
	Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution. [My Copy] Biochemistry, Vol. 37, No. 45. (10 November 1998), pp. 15981-15989. by N. Campobasso, C. A. Costello, C. Kinsland, T. P. Begley, S. E. Ealick posted to 2thi pdb thesis by nigham on 2008-07-02 12:59:11 as
	Protein intermediate trapped by the simultaneous crystallization process. Crystal structure of an iron-saturated intermediate in the Fe3+ binding pathway of camel lactoferrin at 2.7 a resolution. [My Copy] The Journal of biological chemistry, Vol. 276, No. 39. (28 September 2001), pp. 36817-36823. by J. A. Khan, P. Kumar, A. Srinivasan, T. P. Singh posted to 1i6q pdb thesis by nigham on 2008-07-02 12:57:16 as
	Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 54, No. Pt 6 Pt 2. (1 November 1998), pp. 1319-1335. by G. B. Jameson, B. F. Anderson, G. E. Norris, D. H. Thomas, E. N. Baker posted to 1cb6 pdb thesis by nigham on 2008-07-02 12:54:57 as

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protein	37
structure	31
database	20
mapping	15
uniprot	15
structural-biology	14
sequence	12
comps	10
gpcr	8
major-proposal	8
rhodopsin	8
thesis	8
binding	7
mutation	6
structural-genomics-consortium	6
x-ray	5
application	4
compare	4
data-mining	4
drug-design	4
protein-ligand	4
protein-structure-initiative	4
to	4
wwpdb	4
algorithm	3
als	3
amyloid	3
ctbp	3
docking	3
glycerol	3
nmr	3
ontology	3
rest	3
rna	3
web_service	3
2008	2
3bri	2
3e2b	2
bound	2
casp	2
chemical	2
conformation	2
domain-classification	2
dynein	2
exp	2
experiment	2
high-throughput	2
hydration	2
igf1r	2
interaction	2
jenalib	2
lysozyme	2
maltose	2
melittin	2
membrane	2
minor-proposal	2
mmcif	2
mmdb	2
pdbsum	2
protein-protein	2
protein_structure	2
qacr	2
review	2
similarity	2
sites	2
sm-prot	2
structur	2
structure-searching	2
surface	2
transmembrane	2
trehalose	2
ubiquitin	2
unbound	2
visualization	2
water_slaving	2
xtal_software	2
2000	1
2009	1
beta-propeller	1
binary	1
binarytrehalose	1
ccdc	1
classification	1
crystalviolet	1
drug-discovery	1
ebi	1
folding	1
geometric-hashing	1
hdm2	1
hydrationwater	1
iup	1
larisa-soldatova	1
mdintro	1
pdbe	1
pdf	1
ppi	1
programming	1
protein-structure	1
structure_prediction	1
submm	1

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