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Research article   Open Access Highly Accessed

Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis

Balasundaram Padmanabhan, Shigeyuki Yokoyama, Yoshitaka Bessho BMC Structural Biology 2013, 13:10 (20 May 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access

Helical ambivalency induced by point mutations

Nicholus Bhattacharjee, Parbati Biswas BMC Structural Biology 2013, 13:9 (15 May 2013)

Abstract | Full text | PDF | PubMed

Research article   Open Access Highly Accessed

A structural role for the PHP domain in E. coli DNA polymerase III

Tiago Barros, Joel Guenther, Brian Kelch, Jordan Anaya, Arjun Prabhakar, Mike O’Donnell, John Kuriyan, Meindert H Lamers BMC Structural Biology 2013, 13:8 (14 May 2013)

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

Metal binding can be restored to E. coli polymerase III PHP domain with only three point mutations, demonstrating that the domain structure is highly conserved and is a major structural element of this bacterial replicative polymerase.

Research article   Open Access Highly Accessed

Localization of putative binding sites for cyclic guanosine monophosphate and the anti-cancer drug 5-fluoro-2′-deoxyuridine-5′-monophosphate on ABCC11 in silico models

Mylène Honorat, Raphaël Terreux, Pierre Falson, Attilio Di Pietro, Charles Dumontet, Lea Payen BMC Structural Biology 2013, 13:7 (6 May 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu, Sona Vasudevan BMC Structural Biology 2013, 13:6 (25 April 2013)

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

A new systematic approach for grouping protein structures based upon the type and conformation of the ligand they bind to reveals some unexpected findings and extends the existing structural classification of S-adenosyl-L-13 methionine (SAM) binding proteins

Research article   Open Access Highly Accessed

Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC

Jungwook Kim, Steven C Almo BMC Structural Biology 2013, 13:5 (24 April 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

Shanshan Cui, Yan Wang, Guangju Chen BMC Structural Biology 2013, 13:4 (22 March 2013)

Abstract | Full text | PDF | ePUB | PubMed

Research article   Open Access Highly Accessed

The role of Cysteine 6.47 in class A GPCRs

Mireia Olivella, Gianluigi Caltabiano, Arnau Cordomí BMC Structural Biology 2013, 13:3 (15 March 2013)

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

Analysis of G protein-coupled receptor (GPCR) crystal structures and molecular dynamics simulations of model peptides suggests Cys6.47 is the gate keeper of a hydrogen bond network involving residues known to be crucial to receptor activation.

Research article   Open Access Highly Accessed

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 | Full text | PDF | PubMed

Reviewer acknowledgement   Open Access Highly Accessed

Annual acknowledgement of manuscript reviewers

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

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Research article   Open Access Highly Accessed

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)

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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.

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