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Proteins-Structure Function and Bioinformatics

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Overview

articles

  • Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies.  85:1994-2008. 2017
  • Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis.  84:316-331. 2016
  • Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262.  83:590-596. 2015
  • Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains.  82:3079-3089. 2014
  • Antibody modeling assessment II. Structures and models.  82:1563-1582. 2014
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5.  82:2770-2782. 2014
  • Crystal structure determination of anti-DNA Fab A52.  82:1674-1678. 2014
  • Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site.  82:164-170. 2014
  • Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family.  82:1086-1092. 2014
  • Crystal structure of the C-terminal domain of mouse TLR9.  82:2874-2878. 2014
  • Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe.  82:216-229. 2014
  • The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins.  82:1210-1218. 2014
  • Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase.  81:40-52. 2013
  • Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase.  80:2178-2190. 2012
  • Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.  80:1545-1559. 2012
  • A new regulatory switch in a JAK protein kinase.  79:393-401. 2011
  • Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase.  79:1573-1588. 2011
  • Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.  79:2146-2160. 2011
  • New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap.  78:2571-2586. 2010
  • Thermodynamic resolution: how do errors in modeled protein structures affect binding affinity predictions?.  78:1613-1617. 2010
  • FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.  78:2189-2201. 2010
  • GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex.  78:197-211. 2010
  • Genomics, evolution, and crystal structure of a new family of bacterial spore kinases.  78:1470-1482. 2010
  • Predicting structurally conserved contacts for homologous proteins using sequence conservation filters.  77:448-453. 2009
  • Tuning the conformational properties of the prion peptide.  76:213-225. 2009
  • Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution.  75:296-307. 2009
  • Crystal structure of a novel archaeal AAA plus ATPase SSO 1545 from Sulfolobus solfataricus.  74:1041-1049. 2009
  • Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution.  75:264-271. 2009
  • Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa.  77:559-569. 2009
  • Shape complementarity of protein-protein complexes at multiple resolutions.  75:453-467. 2009
  • Improved model building and assessment of the Calcium-sensing receptor transmembrane domain.  71:215-226. 2008
  • A novel method to map and compare protein-protein interactions in spherical viral capsids.  73:644-655. 2008
  • Automated prediction of ligand-binding sites in proteins.  70:1506-1517. 2008
  • Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts.  71:982-994. 2008
  • Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 Å resolution.  70:603-608. 2008
  • Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 Å resolution.  71:1042-1049. 2008
  • Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM 1506), from Thermatoga maritima at 2.70 Å resolution.  71:1546-1552. 2008
  • Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold.  71:1589-1596. 2008
  • In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the opca outer membrane adhesin.  71:24-34. 2008
  • Loop modeling: sampling, filtering, and scoring.  70:834-843. 2008
  • Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.  72:1171-1188. 2008
  • Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy3-keto-5-methylthiopentenyl-1-phosphate.  69:433-439. 2007
  • Crystal structure of NMA 1982 from Neisseria meningiddis at 1.5 Å resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.  69:415-421. 2007
  • Crystal structure of TM1030 from THermotoga maritima at 2.3 Å resolution reveals molecular details of its transcription repressor function.  68:418-424. 2007
  • Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 Å resolution.  67:247-252. 2007
  • Crystal structure of homoserine o-succinyltransferase from bacillus cereus at 2.4 Å resolution.  68:999-1005. 2007
  • Crystal structures of two novel dye-decolorizing peroxidases reveal a β-barrel fold with a conserved heme-binding motif.  69:223-233. 2007
  • Flipdock: Docking flexible ligands into flexible receptors.  68:726-737. 2007
  • Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.  69:234-243. 2007
  • Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments.  64:629-642. 2006
  • Comparative structural analysis of a novel glutathione S-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 Å resolution.  65:527-537. 2006
  • Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 Å resolution reveals a new fold with a novel active site.  65:771-776. 2006
  • Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.  63:1112-1118. 2006
  • Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold.  65:243-248. 2006
  • Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 a resolution.  63:256-260. 2006
  • Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 a resolution.  64:808-813. 2006
  • Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 Å resolution reveals a fold similar to the Ran-binding protein Mog1p.  65:777-782. 2006
  • Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from thermotoga maritima at 1.90 Å resolution.  65:249-254. 2006
  • Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å-resolution.  63:1106-1111. 2006
  • Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution.  64:1083-1090. 2006
  • Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 Å resolution reveals a new fold.  62:292-296. 2006
  • Receptor rigidity and ligand mobility in trypsin-ligand complexes.  58:407-417. 2005
  • Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution.  61:669-673. 2005
  • Crystal structure of S-adenosylmethionine : tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold.  59:869-874. 2005
  • Crystal structure of a conserved hypothetical protein (gi : 13879369) from Mouse at 1.90 A resolution reveals a new fold.  61:1132-1136. 2005
  • Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold.  58:976-981. 2005
  • Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 Å resolution reveals a new fold.  61:444-448. 2005
  • Crystal structure of an Apo mRNA decapping enzyme (DcpS) from mouse at 1.83 Å resolution.  60:797-802. 2005
  • Crystal structure of an alanine-glyoxylate aminotransferase from anabaena sp at 1.70 A resolution reveals a noncovalently linked PLP cofactor.  58:971-975. 2005
  • Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 Å resolution.  58:755-758. 2005
  • Crystal structure of an indigoidine synthase A (IndA)-like protein (TM64) from Thermotoga maritima at 1.90 A resolution reveals a new fold.  59:864-868. 2005
  • Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold.  61:449-453. 2005
  • Extent of protein-protein interactions and quasi-equivalence in viral capsids.  58:472-477. 2005
  • Nmr structure determination of the conserved hypothetical protein tm1816 from thermotoga maritima.  60:552-557. 2005
  • Nmr structure of the conserved hypothetical protein tm0979 from thermotoga maritima.  59:387-390. 2005
  • Poly-(l-alanine) expansions form core beta-sheets that nucleate amyloid assembly.  61:579-589. 2005
  • An electrostatic basis for the stability of thermophilic proteins.  57:128-141. 2004
  • Predicting interactions of winged-helix transcription factors with DNA.  57:172-187. 2004
  • The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase.  57:444-457. 2004
  • Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution.  56:387-391. 2004
  • Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution.  56:404-408. 2004
  • Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 Å resolution.  56:167-170. 2004
  • Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution.  56:396-400. 2004
  • Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 Å resolution.  56:615-618. 2004
  • Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 Å resolution.  56:611-614. 2004
  • Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77 Å resolution.  55:474-478. 2004
  • Crystal structure of a putative NADPH-dependent oxidoreductase (GI : 18204011) from mouse at 2.10 Å resolution.  56:629-633. 2004
  • Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 Å resolution.  54:810-813. 2004
  • Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 Å resolution.  54:801-805. 2004
  • Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution.  56:392-395. 2004
  • Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 Å resolution.  56:171-175. 2004
  • Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 Å resolution.  57:213-217. 2004
  • Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 Å resolution.  55:768-771. 2004
  • Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 Å resolution.  54:806-809. 2004
  • Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 Å resolution.  55:1078-1081. 2004
  • Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 Å resolution.  56:619-624. 2004
  • Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 Å resolution.  55:759-763. 2004
  • Crystal structure of an orphan protein (TM0875) from thermotoga maritima at 2.00 Å resolution reveals a new fold.  56:607-610. 2004
  • Cryptic epitopes in n-terminally truncated prion protein are exposed in the full-length molecule: Dependence of conformation on ph.  44:110-118. 2001
  • Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation.  42:279-293. 2001
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Identity

International Standard Serial Number (ISSN)

  • 0887-3585

Electronic International Standard Serial Number (EISSN)

  • 1097-0134

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