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		Research article Analysis of proteins with the 'hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins Lakshmi S Pidugu, Koustav Maity, Karthikeyan Ramaswamy, Namita Surolia, Kaza Suguna BMC Structural Biology 2009, 9:37 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF Meiying Zheng, Tomasz Cierpicki, Ko Momotani, Mykhaylo V Artamonov, Urszula Derewenda, John H Bushweller, Avril V Somlyo, Zygmunt S Derewenda BMC Structural Biology 2009, 9:36 (21 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information Pascal Benkert, Torsten Schwede, Silvio CE Tosatto BMC Structural Biology 2009, 9:35 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Universal partitioning of the hierarchical fold network of 50-residue segments in proteins Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii, Junichi Higo BMC Structural Biology 2009, 9:34 (20 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Improving protein structure similarity searches using domain boundaries based on conserved sequence information Kenneth Thompson, Yanli Wang, Tom Madej, Stephen H Bryant BMC Structural Biology 2009, 9:33 (19 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein C Leong Ng, David G Waterman, Eugene V Koonin, Alison D Walters, James PJ Chong, Michail N Isupov, Andrey A Lebedev, David HJ Bunka, Peter G Stockley, Miguel Ortiz-Lombardía, Alfred A Antson BMC Structural Biology 2009, 9:32 (19 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Interaction of perfluorooctanoic acid with human serum albumin Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen, Ling Chen BMC Structural Biology 2009, 9:31 (14 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad BMC Structural Biology 2009, 9:30 (13 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Three dimensional shape comparison of flexible proteins using the local-diameter descriptor Yi Fang, Yu-Shen Liu, Karthik Ramani BMC Structural Biology 2009, 9:29 (12 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Improving consensus contact prediction via server correlation reduction Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li BMC Structural Biology 2009, 9:28 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using an optimal linear combination of six leading threading programs, a novel programming model for protein structure refinement increases the accuracy of inter-residue contact prediction and offers a significant improvement over traditional consensus methods.
		Software PTools: an opensource molecular docking library Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias BMC Structural Biology 2009, 9:27 (1 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Takashi Gojobori, Ken Nishikawa BMC Structural Biology 2009, 9:26 (30 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method validates the premise that low protein sequence conservation and unaligned sequences indicate an intrinsically disordered (ID) structure, and is used to achieve a more accurate identification of ID regions in human transcription factors.
		Research article Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis Hemajit Singh, Shandar Ahmad BMC Structural Biology 2009, 9:25 (27 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs Arvind Marathe, Deepti Karandur, Manju Bansal BMC Structural Biology 2009, 9:24 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Methodology article Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis Gergely Csaba, Fabian Birzele, Ralf Zimmer BMC Structural Biology 2009, 9:23 (17 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new consistent benchmark set reduces errors in protein structure prediction and comparison, which occur when using the SCOP and CATH databases due to large differences in their domain definitions and fold space partitioning.
		Research article Analysis of the impact of solvent on contacts prediction in proteins Sergey A Samsonov, Joan Teyra, Gerd Anders, M Teresa Pisabarro BMC Structural Biology 2009, 9:22 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control Veljko Veljkovic, Nevena Veljkovic, Claude P Muller, Sybille Müller, Sanja Glisic, Vladimir Perovic, Heinz Köhler BMC Structural Biology 2009, 9:21 (7 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Relationship between chemical shift value and accessible surface area for all amino acid atoms Wim F Vranken, Wolfgang Rieping BMC Structural Biology 2009, 9:20 (2 April 2009) Abstract \| Full text \| PDF \| PubMed
		Software ProteinShader: illustrative rendering of macromolecules Joseph R Weber BMC Structural Biology 2009, 9:19 (30 March 2009) Abstract \| Full text \| PDF \| PubMed
		Methodology article Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra Carlos Sorzano, Abraham Otero, Estefanía M Olmos, José Carazo BMC Structural Biology 2009, 9:18 (26 March 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins Outi Heikkinen, Raili Seppala, Helena Tossavainen, Sami Heikkinen, Harri Koskela, Perttu Permi, Ilkka Kilpeläinen BMC Structural Biology 2009, 9:17 (24 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study Maria A Argiriadi, Silvino Sousa, David Banach, Douglas Marcotte, Tao Xiang, Medha J Tomlinson, Megan Demers, Christopher Harris, Silvia Kwak, Jennifer Hardman, Margaret Pietras, Lisa Quinn, Jennifer DiMauro, Baofu Ni, John Mankovich, David W Borhani, Robert V Talanian, Ramkrishna Sadhukhan BMC Structural Biology 2009, 9:16 (18 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A rational mutagenesis approach to structure-based drug design for the promising target MAPKAP Kinase 2 (MK2) has successfully generated multiple well-diffracting crystals, and a primary crystal MK2 structure bound to an ATP-competitive inhibitor.
		Methodology article Structural pattern matching of nonribosomal peptides Ségolène Caboche, Maude Pupin, Valérie Leclère, Phillipe Jacques, Gregory Kucherov BMC Structural Biology 2009, 9:15 (18 March 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani, Giuseppe Pizzorno BMC Structural Biology 2009, 9:14 (16 March 2009) Abstract \| Full text \| PDF \| PubMed
		Database Database of ligand-induced domain movements in enzymes Guoying Qi, Steven Hayward BMC Structural Biology 2009, 9:13 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To improve our understanding of ligand-induced domain movements in enzymes, a new database 'DynDom' now lists all protein domain movements of crystallographic enzyme-ligand pairs found in the Protein Data Bank.

	All
		Research article Analysis of proteins with the 'hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins Lakshmi S Pidugu, Koustav Maity, Karthikeyan Ramaswamy, Namita Surolia, Kaza Suguna BMC Structural Biology 2009, 9:37 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF Meiying Zheng, Tomasz Cierpicki, Ko Momotani, Mykhaylo V Artamonov, Urszula Derewenda, John H Bushweller, Avril V Somlyo, Zygmunt S Derewenda BMC Structural Biology 2009, 9:36 (21 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information Pascal Benkert, Torsten Schwede, Silvio CE Tosatto BMC Structural Biology 2009, 9:35 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Universal partitioning of the hierarchical fold network of 50-residue segments in proteins Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii, Junichi Higo BMC Structural Biology 2009, 9:34 (20 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Improving protein structure similarity searches using domain boundaries based on conserved sequence information Kenneth Thompson, Yanli Wang, Tom Madej, Stephen H Bryant BMC Structural Biology 2009, 9:33 (19 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein C Leong Ng, David G Waterman, Eugene V Koonin, Alison D Walters, James PJ Chong, Michail N Isupov, Andrey A Lebedev, David HJ Bunka, Peter G Stockley, Miguel Ortiz-Lombardía, Alfred A Antson BMC Structural Biology 2009, 9:32 (19 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Interaction of perfluorooctanoic acid with human serum albumin Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen, Ling Chen BMC Structural Biology 2009, 9:31 (14 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad BMC Structural Biology 2009, 9:30 (13 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Three dimensional shape comparison of flexible proteins using the local-diameter descriptor Yi Fang, Yu-Shen Liu, Karthik Ramani BMC Structural Biology 2009, 9:29 (12 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Improving consensus contact prediction via server correlation reduction Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li BMC Structural Biology 2009, 9:28 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using an optimal linear combination of six leading threading programs, a novel programming model for protein structure refinement increases the accuracy of inter-residue contact prediction and offers a significant improvement over traditional consensus methods.
		Software PTools: an opensource molecular docking library Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias BMC Structural Biology 2009, 9:27 (1 May 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Takashi Gojobori, Ken Nishikawa BMC Structural Biology 2009, 9:26 (30 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method validates the premise that low protein sequence conservation and unaligned sequences indicate an intrinsically disordered (ID) structure, and is used to achieve a more accurate identification of ID regions in human transcription factors.
		Research article Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis Hemajit Singh, Shandar Ahmad BMC Structural Biology 2009, 9:25 (27 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs Arvind Marathe, Deepti Karandur, Manju Bansal BMC Structural Biology 2009, 9:24 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Methodology article Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis Gergely Csaba, Fabian Birzele, Ralf Zimmer BMC Structural Biology 2009, 9:23 (17 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new consistent benchmark set reduces errors in protein structure prediction and comparison, which occur when using the SCOP and CATH databases due to large differences in their domain definitions and fold space partitioning.
		Research article Analysis of the impact of solvent on contacts prediction in proteins Sergey A Samsonov, Joan Teyra, Gerd Anders, M Teresa Pisabarro BMC Structural Biology 2009, 9:22 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control Veljko Veljkovic, Nevena Veljkovic, Claude P Muller, Sybille Müller, Sanja Glisic, Vladimir Perovic, Heinz Köhler BMC Structural Biology 2009, 9:21 (7 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Relationship between chemical shift value and accessible surface area for all amino acid atoms Wim F Vranken, Wolfgang Rieping BMC Structural Biology 2009, 9:20 (2 April 2009) Abstract \| Full text \| PDF \| PubMed
		Software ProteinShader: illustrative rendering of macromolecules Joseph R Weber BMC Structural Biology 2009, 9:19 (30 March 2009) Abstract \| Full text \| PDF \| PubMed
		Methodology article Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra Carlos Sorzano, Abraham Otero, Estefanía M Olmos, José Carazo BMC Structural Biology 2009, 9:18 (26 March 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins Outi Heikkinen, Raili Seppala, Helena Tossavainen, Sami Heikkinen, Harri Koskela, Perttu Permi, Ilkka Kilpeläinen BMC Structural Biology 2009, 9:17 (24 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study Maria A Argiriadi, Silvino Sousa, David Banach, Douglas Marcotte, Tao Xiang, Medha J Tomlinson, Megan Demers, Christopher Harris, Silvia Kwak, Jennifer Hardman, Margaret Pietras, Lisa Quinn, Jennifer DiMauro, Baofu Ni, John Mankovich, David W Borhani, Robert V Talanian, Ramkrishna Sadhukhan BMC Structural Biology 2009, 9:16 (18 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A rational mutagenesis approach to structure-based drug design for the promising target MAPKAP Kinase 2 (MK2) has successfully generated multiple well-diffracting crystals, and a primary crystal MK2 structure bound to an ATP-competitive inhibitor.
		Methodology article Structural pattern matching of nonribosomal peptides Ségolène Caboche, Maude Pupin, Valérie Leclère, Phillipe Jacques, Gregory Kucherov BMC Structural Biology 2009, 9:15 (18 March 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani, Giuseppe Pizzorno BMC Structural Biology 2009, 9:14 (16 March 2009) Abstract \| Full text \| PDF \| PubMed
		Database Database of ligand-induced domain movements in enzymes Guoying Qi, Steven Hayward BMC Structural Biology 2009, 9:13 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To improve our understanding of ligand-induced domain movements in enzymes, a new database 'DynDom' now lists all protein domain movements of crystallographic enzyme-ligand pairs found in the Protein Data Bank.