articles
- Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic 2021
- 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
- Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 82:2770-2782. 2014
- Crystal structure of the C-terminal domain of mouse TLR9. 82:2874-2878. 2014
- Antibody modeling assessment II. Structures and models. 82:1563-1582. 2014
- Crystal structure determination of anti-DNA Fab A52. 82:1674-1678. 2014
- The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins. 82:1210-1218. 2014
- Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. 82:1086-1092. 2014
- Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. 82:216-229. 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
- 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
- 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
- Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase. 79:1573-1588. 2011
- A new regulatory switch in a JAK protein kinase. 79:393-401. 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
- FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. 78:2189-2201. 2010
- Thermodynamic resolution: how do errors in modeled protein structures affect binding affinity predictions?. 78:1613-1617. 2010
- Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. 78:1470-1482. 2010
- Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. 78:3205-3211. 2010
- GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. 78:197-211. 2010
- Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa. 77:559-569. 2009
- 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
- Shape complementarity of protein-protein complexes at multiple resolutions. 75:453-467. 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
- A novel method to map and compare protein-protein interactions in spherical viral capsids. 73:644-655. 2008
- Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. 72:1171-1188. 2008
- Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold. 71:1589-1596. 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 AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 Å resolution. 71:1042-1049. 2008
- Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. 71:215-226. 2008
- In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the opca outer membrane adhesin. 71:24-34. 2008
- Automated prediction of ligand-binding sites in proteins. 70:1506-1517. 2008
- Loop modeling: sampling, filtering, and scoring. 70:834-843. 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 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 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 structures of two novel dye-decolorizing peroxidases reveal a β-barrel fold with a conserved heme-binding motif. 69:223-233. 2007
- Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. 69:234-243. 2007
- Crystal structure of homoserine o-succinyltransferase from bacillus cereus at 2.4 Å resolution. 68:999-1005. 2007
- Flipdock: Docking flexible ligands into flexible receptors. 68:726-737. 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 NMA 1982 from Neisseria meningiddis at 1.5 Å resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases. 69:415-421. 2007
- 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 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 a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold. 65:243-248. 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 the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution. 64:1083-1090. 2006
- Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 a resolution. 64:808-813. 2006
- Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments. 64:629-642. 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 phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å-resolution. 63:1106-1111. 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 virulence factor CJ0248 from Campylobacter jejuni at 2.25 Å resolution reveals a new fold. 62:292-296. 2006
- 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 Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution. 61:669-673. 2005
- Poly-(l-alanine) expansions form core beta-sheets that nucleate amyloid assembly. 61:579-589. 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 the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold. 61:449-453. 2005
- Crystal structure of an Apo mRNA decapping enzyme (DcpS) from mouse at 1.83 Å resolution. 60:797-802. 2005
- Nmr structure determination of the conserved hypothetical protein tm1816 from thermotoga maritima. 60:552-557. 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 an indigoidine synthase A (IndA)-like protein (TM64) from Thermotoga maritima at 1.90 A resolution reveals a new fold. 59:864-868. 2005
- Nmr structure of the conserved hypothetical protein tm0979 from thermotoga maritima. 59:387-390. 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 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
- Extent of protein-protein interactions and quasi-equivalence in viral capsids. 58:472-477. 2005
- Receptor rigidity and ligand mobility in trypsin-ligand complexes. 58:407-417. 2005
- The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. 57:444-457. 2004
- An electrostatic basis for the stability of thermophilic proteins. 57:128-141. 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
- Predicting interactions of winged-helix transcription factors with DNA. 57:172-187. 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 putative NADPH-dependent oxidoreductase (GI : 18204011) from mouse at 2.10 Å resolution. 56:629-633. 2004
- Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 Å resolution. 56:619-624. 2004
- Crystal structure of an orphan protein (TM0875) from thermotoga maritima at 2.00 Å resolution reveals a new fold. 56:607-610. 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 methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution. 56:396-400. 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 glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 Å resolution. 56:167-170. 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 an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 Å resolution. 55:1078-1081. 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 aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 Å resolution. 55:759-763. 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 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 an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 Å resolution. 54:806-809. 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