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Research article   Open Access

Designing and benchmarking the MULTICOM protein structure prediction system

Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng BMC Structural Biology 2013, 13:2 (27 February 2013)

Abstract | Provisional PDF | PubMed

Reviewer acknowledgement   Open Access

Annual acknowledgement of manuscript reviewers

Simon Harold BMC Structural Biology 2013, 13:1 (19 February 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them

Volodymyr O Kitam, Oksana V Maksymchuk, Mykola O Chashchyn BMC Structural Biology 2012, 12:33 (17 December 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure

Jaeok Park, Yih-Shyan Lin, Joris W De Schutter, Youla S Tsantrizos, Albert M Berghuis BMC Structural Biology 2012, 12:32 (12 December 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Three crystal structures of human farnesyl pyrophosphate synthase (FPPS) in ternary complex with a novel bisphosphonate inhibitor reveal mechanistic insight of the conformational change in the C-terminal tail closure that is essential for catalysis.

Software   Open Access Highly Accessed

Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling

Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov BMC Structural Biology 2012, 12:31 (5 December 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Protein Nano-Object Integrator (ProNOI) is a novel software tool for generating atomic-style nano shapes in conjunction with biological macromolecules, allowing users to manipulate shape, dimension and position, and charge objects with user-specified charge density.

Research article   Open Access Highly Accessed

Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii

Yap Boon Wooi Tommy, Theam Soon Lim, Rahmah Noordin, Geita Saadatnia, Yee Siew Choong BMC Structural Biology 2012, 12:30 (27 November 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The 3D structure of the 12 kDa excretory-secretory protein of Toxoplasma gondii reveals a thioredoxin-like backbone and three potential epitopes functioning as a single antibody binding site, aiding the development of an antigen detection test for toxoplasmosis.

Methodology article   Open Access

MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry

Janosch Hennig, Sjoerd J de Vries, Klaus DM Hennig, Leah Randles, Kylie J Walters, Maria Sunnerhagen, Alexandre MJJ Bonvin BMC Structural Biology 2012, 12:29 (15 November 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR

Govindarajan Sudha, Subburaj Yamunadevi, Nidhi Tyagi, Saumitra Das, Narayanaswamy Srinivasan BMC Structural Biology 2012, 12:28 (13 November 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Evolutionarily consistent families in SCOP: sequence, structure and function

Ralph B Pethica, Michael Levitt, Julian Gough BMC Structural Biology 2012, 12:27 (18 October 2012)

Abstract | Full text | PDF | PubMed

Software   Open Access Highly Accessed

Structure Motivator: A tool for exploring small three-dimensional elements in proteins

David P Leader, E Milner-White BMC Structural Biology 2012, 12:26 (16 October 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex

Lorena Novoa-Aponte, Andrés León-Torres, Miyer Patiño-Ruiz, Jenifer Cuesta-Bernal, Luz-Mary Salazar, David Landsman, Leonardo Mariño-Ramírez, Carlos-Yesid Soto BMC Structural Biology 2012, 12:25 (3 October 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Sagar Chittori, Handanahal S Savithri, Mathur RN Murthy BMC Structural Biology 2012, 12:24 (2 October 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation

Xiuhua Liu, Jing Gong, Tiandi Wei, Zhi Wang, Qian Du, Deyu Zhu, Yan Huang, Sujuan Xu, Lichuan Gu BMC Structural Biology 2012, 12:23 (26 September 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Structural mismatch between the only heme storage protein of Vibrio cholera, HutZ, and its homologous protein HugZ, suggests that deficiency in heme oxygenase activity might derive from a single residue shift.

Research article   Open Access Highly Accessed

Enabling structure-based drug design of Tyk2 through co-crystallization with a stabilizing aminoindazole inhibitor

Maria A Argiriadi, Eric R Goedken, David Banach, David W Borhani, Andrew Burchat, Richard W Dixon, Doug Marcotte, Gary Overmeyer, Valerie Pivorunas, Ramkrishna Sadhukhan, Silvino Sousa, Nigel St Moore, Medha Tomlinson, Jeffrey Voss, Lu Wang, Neil Wishart, Kevin Woller, Robert V Talanian BMC Structural Biology 2012, 12:22 (20 September 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The mouse Tyk2 protein kinase complexed to an ATP-competitive 3-aminoindazole inhibitor is stabilized relative to the unliganded enzyme, with the crystal structure revealing key differences in the glycine-rich loop conformation compared to those in human orthologs.

Research article   Open Access Highly Accessed

Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)

Shu Liu, Rao Fu, Xiao Cheng, Sheng-Ping Chen, Li-Hua Zhou BMC Structural Biology 2012, 12:21 (27 August 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study

Atanas Patronov, Ivan Dimitrov, Darren R Flower, Irini Doytchinova BMC Structural Biology 2012, 12:20 (5 August 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

A three-dimensional topology of complex I inferred from evolutionary correlations

Philip R Kensche, Isabel Duarte, Martijn A Huynen BMC Structural Biology 2012, 12:19 (3 August 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Co-evolution of proteins can be used to predict the 3D arrangement of subunits in a multi-protein complex, with more than 60% of the evolutionary correlation among subunits in eukaryotic complex I explained by physical distance.

Research article   Open Access Highly Accessed

Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type

Kazuo Fujiwara, Hiromi Toda, Masamichi Ikeguchi BMC Structural Biology 2012, 12:18 (2 August 2012)

Abstract | Full text | PDF | PubMed

Review   Open Access Highly Accessed

Integrative structural modeling with small angle X-ray scattering profiles

Dina Schneidman-Duhovny, Seung Kim, Andrej Sali BMC Structural Biology 2012, 12:17 (16 July 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Dina Schneidman-Duhovny and colleagues review the use of Small-Angle X-ray Scattering (SAXS) profiles for the structural modeling of proteins, nucleic acids and their complexes, and propose an integrative approach combining multiple datasets to help discriminate among ambiguous models.

Research article   Open Access Highly Accessed

Structural characterization of S100A15 reveals a novel zinc coordination site among S100 proteins and altered surface chemistry with functional implications for receptor binding

Jill I Murray, Michelle L Tonkin, Amanda L Whiting, Fangni Peng, Benjamin Farnell, Jay T Cullen, Fraser Hof, Martin J Boulanger BMC Structural Biology 2012, 12:16 (2 July 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase

Yuji Ashikawa, Zui Fujimoto, Yusuke Usami, Kengo Inoue, Haruko Noguchi, Hisakazu Yamane, Hideaki Nojiri BMC Structural Biology 2012, 12:15 (24 June 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family

Apirat Chaikuad, Ewa S Pilka, Antonio De Riso, Frank von Delft, Kathryn L Kavanagh, Catherine Vénien-Bryan, Udo Oppermann, Wyatt W Yue BMC Structural Biology 2012, 12:14 (21 June 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD

Madeleine Schreiner, Hartmut H Niemann BMC Structural Biology 2012, 12:13 (18 June 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Conservation and divergence between cytoplasmic and muscle-specific actin capping proteins: insights from the crystal structure of cytoplasmic Cap32/34 from Dictyostelium discoideum

Christian Eckert, Agnieszka Goretzki, Maria Faberova, Martin Kollmar BMC Structural Biology 2012, 12:12 (1 June 2012)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

Wataru Nemoto, Hiroyuki Toh BMC Structural Biology 2012, 12:11 (29 May 2012)

Abstract | Full text | PDF | PubMed

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