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Research articles Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases Balachandran Manavalan, Senthil K Murugapiran, Gwang Lee, and Sangdun Choi PMCID: PMC2835699 Crystal structure of the signaling helix coiled-coil domain of the β1 subunit of the soluble guanylyl cyclase Xiaolei Ma, Annie Beuve, and Focco van den Akker PMCID: PMC2828450 Analysis of the role of PCNA-DNA contacts during clamp loading Randall McNally, Gregory D Bowman, Eric R Goedken, Mike O'Donnell, and John Kuriyan PMCID: PMC2824762 Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues Shirley Wu, Tianyun Liu, and Russ B Altman PMCID: PMC2833161 Modeling of loops in proteins: a multi-method approach Michal Jamroz and Andrzej Kolinski PMCID: PMC2837870 Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase Ambarnil Ghosh, Ashesh Nandy, and Papiya Nandy PMCID: PMC2836360 Structural investigation of zymogenic and activated forms of human blood coagulation factor VIII: a computational molecular dynamics study Divi Venkateswarlu PMCID: PMC2837666 Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach Chiara Parravicini, Maria P Abbracchio, Piercarlo Fantucci, and Graziella Ranghino PMCID: PMC2850907 Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery Alejandro Panjkovich and Xavier Daura PMCID: PMC2864279 The structure of a reduced form of OxyR from Neisseria meningitidis Sarah Sainsbury, Jingshan Ren, Joanne E Nettleship, Nigel J Saunders, David I Stuart, and Raymond J Owens PMCID: PMC2881104 Elastic network model of allosteric regulation in protein kinase PDK1 Gareth Williams PMCID: PMC2888814 Progesterone modulation of transmembrane helix-helix interactions between the α-subunit of Na/K-ATPase and phospholipid N-methyltransferase in the oocyte plasma membrane Gene A Morrill, Adele B Kostellow, and Amir Askari PMCID: PMC2887865 Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains Louise E Bird, Jingshan Ren, Joanne E Nettleship, Gert E Folkers, Raymond J Owens, and David K Stammers PMCID: PMC2893186 Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor Gianpiero Garau, Laura Muzzolini, Paola Tornaghi, and Massimo Degano PMCID: PMC2898832 Solution structure of the human signaling protein RACK1 Kaliandra A Gonçalves, Julio C Borges, Julio C Silva, Priscila F Papa, Gustavo C Bressan, Iris L Torriani, and Jörg Kobarg PMCID: PMC2896345 Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase Stephen M Soisson, Sangita B Patel, Pravien D Abeywickrema, Noel J Byrne, Ronald E Diehl, Dawn L Hall, Rachael E Ford, John C Reid, Keith W Rickert, Jennifer M Shipman, Sujata Sharma, and Kevin J Lumb PMCID: PMC2893456 Research Articles Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures Rupali A Gadkari and Narayanaswamy Srinivasan PMCID: PMC2906493 Novel topological descriptors for analyzing biological networks Matthias M Dehmer, Nicola N Barbarini, Kurt K Varmuza, and Armin A Graber PMCID: PMC2906494 A kinesin motor in a force-producing conformation Elisabeth Heuston, C Eric Bronner, F Jon Kull, and Sharyn A Endow PMCID: PMC2906495 Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone Michael L Barta, Lingling Zhang, Wendy L Picking, and Brian V Geisbrecht PMCID: PMC2912912 Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d Andrew C Doxey, Zhenyu Cheng, Barbara A Moffatt, and Brendan J McConkey PMCID: PMC2924342 Systematic analysis of short internal indels and their impact on protein folding RyangGuk Kim and Jun-tao Guo PMCID: PMC2924343 Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2ΔGF122) and structural roles of F122 in target recognition Tatsutoshi Inuzuka, Hironori Suzuki, Masato Kawasaki, Hideki Shibata, Soichi Wakatsuki, and Masatoshi Maki PMCID: PMC2927601 Comparing interfacial dynamics in protein-protein complexes: an elastic network approach Andrea Zen, Cristian Micheletti, Ozlem Keskin, and Ruth Nussinov PMCID: PMC2927602 Methodology Article Improving predicted protein loop structure ranking using a Pareto-optimality consensus method Yaohang Li, Ionel Rata, See-wing Chiu, and Eric Jakobsson PMCID: PMC2914074 Other Issues: Journal List
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