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BMC Structural Biology

ISSN: 1472--6807
Publisher: BioMed Central


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Sequence periodicity in nucleosomal DNA and intrinsic curvature

Author(s): Nair T Murlidharan
Volume: 10
Issue: Suppl 1
Year: 2010
Protein structure determination via an efficient geometric build-up algorithm

Author(s): Davis Robert | Ernst Claus | Wu Di
Volume: 10
Issue: Suppl 1
Year: 2010
Mining for the antibody-antigen interacting associations that predict the B cell epitopes

Author(s): Zhao Liang | Li Jinyan
Volume: 10
Issue: Suppl 1
Year: 2010
Structural interpretation of protein-protein interaction network

Author(s): Katebi Ataur | Kloczkowski Andrzej | Jernigan Robert
Volume: 10
Issue: Suppl 1
Year: 2010
Generalized spring tensor models for protein fluctuation dynamics and conformation changes

Author(s): Lin Tu-Liang | Song Guang
Volume: 10
Issue: Suppl 1
Year: 2010
Tracing conformational changes in proteins

Author(s): Haspel Nurit | Moll Mark | Baker Matthew | Chiu Wah | Kavraki Lydia
Volume: 10
Issue: Suppl 1
Year: 2010
Discrimination of thermophilic and mesophilic proteins

Author(s): Taylor Todd | Vaisman Iosif
Volume: 10
Issue: Suppl 1
Year: 2010
The 3rd Computational Structural Bioinformatics Workshop

Author(s): He Jing | Wu Di
Volume: 10
Issue: Suppl 1
Year: 2010
Dynamical Basis for Drug Resistance of HIV-1 Protease

Author(s): Mao Yi
Volume: 11
Issue: 1
Year: 2011
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach

Author(s): Patronov Atanas | Dimitrov Ivan | Flower Darren | Doytchinova Irini
Volume: 11
Issue: 1
Year: 2011
Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1

Author(s): Yuan Cai | Chen Liqing | Meehan Edward | Daly Norelle | Craik David | Huang Mingdong | Ngo Jacky
Volume: 11
Issue: 1
Year: 2011
Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like structural family

Author(s): Clarke Teresa | Romanov Vladimir | Chirgadze Yuri | Klomsiri Chananat | Kisselman Gera | Wu-Brown Jean | Poole Leslie | Pai Emil | Chirgadze Nickolay
Volume: 11
Issue: 1
Year: 2011
Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

Author(s): Isvoran Adriana | Badel Anne | Craescu Constantin | Miron Simona | Miteva Maria
Volume: 11
Issue: 1
Year: 2011
A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers

Author(s): Gamliel Roi | Kedem Klara | Kolodny Rachel | Keasar Chen
Volume: 11
Issue: 1
Year: 2011
Analysis of the unique structural and physicochemical properties of the DraD/AfaD invasin in the context of its belonging to the family of chaperone/usher type fimbrial subunits

Author(s): Piątek Rafał | Bruździak Piotr | Zalewska-Piątek Beata | Wojciechowski Marek | Namieśnik Justyna | Kur Józef
Volume: 11
Issue: 1
Year: 2011
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

Author(s): Bracken Colten | Neighbor Amber | Lamlenn Kenneth | Thomas Geoffrey | Schubert Heidi | Whitby Frank | Howard Bruce
Volume: 11
Issue: 1
Year: 2011
Crystallographic analysis reveals the structural basis of the high-affinity binding of iophenoxic acid to human serum albumin

Author(s): Ryan Ali | Chung Chun-wa | Curry Stephen
Volume: 11
Issue: 1
Year: 2011
Gα16 interacts with tetratricopeptide repeat 1 (TPR1) through its β3 region to activate Ras independently of phospholipase Cβ signaling

Author(s): Liu Andrew | Lo Rico | Guo Emily | Ho Maurice | Ye Richard | Wong Yung
Volume: 11
Issue: 1
Year: 2011
Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate

Author(s): Morgan Rachel | Batot Gaëlle | Dement Jennifer | Rao Vincenzo | Eadsforth Thomas | Hunter William
Volume: 11
Issue: 1
Year: 2011
Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity

Author(s): Dawson Alice | Fyfe Paul | Gillet Florian | Hunter William
Volume: 11
Issue: 1
Year: 2011
Binary classification of protein molecules into intrinsically disordered and ordered segments

Author(s): Fukuchi Satoshi | Hosoda Kazuo | Homma Keiichi | Gojobori Takashi | Nishikawa Ken
Volume: 11
Issue: 1
Year: 2011
A model for the Escherichia coli FtsB/FtsL/FtsQ cell division complex

Author(s): Villanelo Felipe | Ordenes Alexis | Brunet Juan | Lagos Rosalba | Monasterio Octavio
Volume: 11
Issue: 1
Year: 2011
Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility

Author(s): Paredes Diana | Watters Kyle | Pitman Derek | Bystroff Christopher | Dordick Jonathan
Volume: 11
Issue: 1
Year: 2011
Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis

Author(s): Edwards Thomas | Abramov Ariel | Smith Eric | Baydo Ruth | Leonard Jess | Leibly David | Thompkins Kaitlin | Clifton Matthew | Gardberg Anna | Staker Bart | Van Voorhis Wesley | Myler Peter | Stewart Lance
Volume: 11
Issue: 1
Year: 2011
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif

Author(s): Er Tze-Kiong | Chen Chih-Chieh | Liu Yen-Yi | Chang Hui-Chiu | Chien Yin-Hsiu | Chang Jan-Gowth | Hwang Jenn-Kang | Jong Yuh-Jyh
Volume: 11
Issue: 1
Year: 2011
Evolutionary traces decode molecular mechanism behind fast pace of myosin XI

Author(s): Syamaladevi Divya | Sowdhamini R
Volume: 11
Issue: 1
Year: 2011
Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

Author(s): Bernini Andrea | Spiga Ottavia | Consonni Roberto | Arosio Ivana | Fusi Paola | Cirri Simone | Guagliardi Annamaria | Niccolai Neri
Volume: 11
Issue: 1
Year: 2011
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

Author(s): Kirillova Svetlana | Carugo Oliviero
Volume: 11
Issue: 1
Year: 2011
A conformation ensemble approach to protein residue-residue contact

Author(s): Eickholt Jesse | Wang Zheng | Cheng Jianlin
Volume: 11
Issue: 1
Year: 2011
Novel dimeric β-helical model of an ice nucleation protein with bridged active sites

Author(s): Garnham Christopher | Campbell Robert | Walker Virginia | Davies Peter
Volume: 11
Issue: 1
Year: 2011
Structural studies of the PARP-1 BRCT domain

Author(s): Loeffler Paul | Cuneo Matthew | Mueller Geoffrey | DeRose Eugene | Gabel Scott | London Robert
Volume: 11
Issue: 1
Year: 2011
Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria

Author(s): Yu Shen | Vit Allegra | Devenish Sean | Mahanty H Khris | Itzen Aymelt | Goody Roger | Blankenfeldt Wulf
Volume: 11
Issue: 1
Year: 2011
Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models

Author(s): Latek Dorota | Kolinski Andrzej
Volume: 8
Issue: 1
Year: 2008
Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

Author(s): Ikeda Kazuyoshi | Hirokawa Takatsugu | Higo Junichi | Tomii Kentaro
Volume: 8
Issue: 1
Year: 2008
Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase

Author(s): Santini Sébastien | Monchois Vincent | Mouz Nicolas | Sigoillot Cécile | Rousselle Tristan | Claverie Jean-Michel | Abergel Chantal
Volume: 8
Issue: 1
Year: 2008
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure

Author(s): Chakravarty Suvobrata | Godbole Sucheta | Zhang Bing | Berger Seth | Sanchez Roberto
Volume: 8
Issue: 1
Year: 2008
Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

Author(s): Bardiaux Benjamin | Bernard Aymeric | Rieping Wolfgang | Habeck Michael | Malliavin Thérèse | Nilges Michael
Volume: 8
Issue: 1
Year: 2008
Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes

Author(s): Xu Zhen | Kohli Ekta | Devlin Karl | Bold Michael | Nix Jay | Misra Saurav
Volume: 8
Issue: 1
Year: 2008
Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches

Author(s): Sayar Kemal | Uğur Özlem | Liu Tong | Hilser Vincent | Onaran Ongun
Volume: 8
Issue: 1
Year: 2008
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Author(s): Sandhya Sankaran | Pankaj Barah | Govind Madabosse | Offmann Bernard | Srinivasan Narayanaswamy | Sowdhamini Ramanathan
Volume: 8
Issue: 1
Year: 2008
Improving the accuracy of template-based predictions by mixing and matching between initial models

Author(s): Liu Tianyun | Guerquin Michal | Samudrala Ram
Volume: 8
Issue: 1
Year: 2008
Protecting role of cosolvents in protein denaturation by SDS: a structural study

Author(s): Michaux Catherine | Pouyez Jenny | Wouters Johan | Privé Gilbert
Volume: 8
Issue: 1
Year: 2008
Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: Towards the design of higher-affinity inhibitors

Author(s): Hazan Corinne | Boudsocq François | Gervais Virginie | Saurel Olivier | Ciais Marion | Cazaux Christophe | Czaplicki Jerzy | Milon Alain
Volume: 8
Issue: 1
Year: 2008
Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain

Author(s): Potter Jane | Randall Richard | Taylor Garry
Volume: 8
Issue: 1
Year: 2008
Charge environments around phosphorylation sites in proteins

Author(s): Kitchen James | Saunders Rebecca | Warwicker Jim
Volume: 8
Issue: 1
Year: 2008
Crystal structures of PI3K-C2α PX domain indicate conformational change associated with ligand binding

Author(s): Parkinson Gary | Vines David | Driscoll Paul | Djordjevic Snezana
Volume: 8
Issue: 1
Year: 2008
Solution structure of the Legionella pneumophila Mip-rapamycin complex

Author(s): Ceymann Andreas | Horstmann Martin | Ehses Philipp | Schweimer Kristian | Paschke Anne-Katrin | Steinert Michael | Faber Cornelius
Volume: 8
Issue: 1
Year: 2008
"Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms

Author(s): Paiardini Alessandro | Sali Riccardo | Bossa Francesco | Pascarella Stefano
Volume: 8
Issue: 1
Year: 2008
A multi-template combination algorithm for protein comparative modeling

Author(s): Cheng Jianlin
Volume: 8
Issue: 1
Year: 2008
Structural deformation upon protein-protein interaction: A structural alphabet approach

Author(s): Martin Juliette | Regad Leslie | Lecornet Hélène | Camproux Anne-Claude
Volume: 8
Issue: 1
Year: 2008
Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms

Author(s): Bleicher Lucas | Aparicio Ricardo | Nunes Fabio | Martinez Leandro | Gomes Dias Sandra | Figueira Ana | Santos Maria | Venturelli Walter | da Silva Rosangela | Donate Paulo | Neves Francisco | Simeoni Luiz | Baxter John | Webb Paul | Skaf Munir | Polikarpov Igor
Volume: 8
Issue: 1
Year: 2008
Comparative modelling by restraint-based conformational sampling

Author(s): Furnham Nicholas | de Bakker Paul | Gore Swanand | Burke David | Blundell Tom
Volume: 8
Issue: 1
Year: 2008
GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures

Author(s): Laborde Thomas | Tomita Masaru | Krishnan Arun
Volume: 8
Issue: 1
Year: 2008
Fast dynamics perturbation analysis for prediction of protein functional sites

Author(s): Ming Dengming | Cohn Judith | Wall Michael
Volume: 8
Issue: 1
Year: 2008
Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure

Author(s): Majava Viivi | Petoukhov Maxim | Hayashi Nobuhiro | Pirilä Päivi | Svergun Dmitri | Kursula Petri
Volume: 8
Issue: 1
Year: 2008
Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle

Author(s): Schenk Gerhard | Elliott Tristan | Leung Eleanor | Carrington Lyle | Mitić Nataša | Gahan Lawrence | Guddat Luke
Volume: 8
Issue: 1
Year: 2008
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling

Author(s): Adam Benoit | Charloteaux Benoit | Beaufays Jerome | Vanhamme Luc | Godfroid Edmond | Brasseur Robert | Lins Laurence
Volume: 8
Issue: 1
Year: 2008
Modeling structure and flexibility of Candida antarctica lipase B in organic solvents

Author(s): Trodler Peter | Pleiss Jürgen
Volume: 8
Issue: 1
Year: 2008
Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes

Author(s): Ma Ze-Qiang | Xie Sheng-Xue | Huang Qing-Qing | Nan Fa-Jun | Hurley Thomas | Ye Qi-Zhuang
Volume: 7
Issue: 1
Year: 2007
The structure of mollusc larval shells formed in the presence of the chitin synthase inhibitor Nikkomycin Z

Author(s): Schönitzer Veronika | Weiss Ingrid
Volume: 7
Issue: 1
Year: 2007
Neutral evolution of Protein-protein interactions: a computational study using simple models

Author(s): Noirel Josselin | Simonson Thomas
Volume: 7
Issue: 1
Year: 2007
Preservation of protein clefts in comparative models

Author(s): Piedra David | Lois Sergi | de la Cruz Xavier
Volume: 8
Issue: 1
Year: 2008
NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin

Author(s): LeMaster David | Anderson Janet | Wang Limin | Guo Yi | Li Hongmin | Hernández Griselda
Volume: 7
Issue: 1
Year: 2007
Self-assembly of human latexin into amyloid-like oligomers

Author(s): Pallarés Irantzu | Berenguer Clara | Avilés Francesc | Vendrell Josep | Ventura Salvador
Volume: 7
Issue: 1
Year: 2007
A comprehensive analysis of non-sequential alignments between all protein structures

Author(s): Abyzov Alexej | Ilyin Valentin
Volume: 7
Issue: 1
Year: 2007
Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone

Author(s): Ramaswamy Amutha | Ioshikhes Ilya
Volume: 7
Issue: 1
Year: 2007
Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog

Author(s): Ku Shao-Yang | Cornell Kenneth | Howell P Lynne
Volume: 7
Issue: 1
Year: 2007
Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

Author(s): Carra John | McHugh Colleen | Mulligan Sheila | Machiesky LeeAnn | Soares Alexei | Millard Charles
Volume: 7
Issue: 1
Year: 2007
Structural disorder promotes assembly of protein complexes

Author(s): Hegyi Hedi | Schad Eva | Tompa Peter
Volume: 7
Issue: 1
Year: 2007
Structural analysis of the carboxy terminal PH domain of pleckstrin bound to D-myo-inositol 1,2,3,5,6-pentakisphosphate

Author(s): Jackson Sean | Zhang Yi | Haslam Richard | Junop Murray
Volume: 7
Issue: 1
Year: 2007
Antibody-protein interactions: benchmark datasets and prediction tools evaluation

Author(s): Ponomarenko Julia | Bourne Philip
Volume: 7
Issue: 1
Year: 2007
Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides

Author(s): Scotter Andrew | Guo Meng | Tomczak Melanie | Daley Margaret | Campbell Robert | Oko Richard | Bateman David | Chakrabartty Avijit | Sykes Brian | Davies Peter
Volume: 7
Issue: 1
Year: 2007
Glutathione mediated regulation of oligomeric structure and functional activity of Plasmodium falciparum glutathione S-transferase

Author(s): Tripathi Timir | Rahlfs Stefan | Becker Katja | Bhakuni Vinod
Volume: 7
Issue: 1
Year: 2007
Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation

Author(s): Porter Corrine | Matthews Jacqueline | Mackay Joel | Pursglove Sharon | Schmidberger Jason | Leedman Peter | Pero Stephanie | Krag David | Wilce Matthew | Wilce Jacqueline
Volume: 7
Issue: 1
Year: 2007
Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+

Author(s): Nascimento Alessandro | Catalano-Dupuy Daniela | Bernardes Amanda | Neto Mario | Santos Maria | Ceccarelli Eduardo | Polikarpov Igor
Volume: 7
Issue: 1
Year: 2007
The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery

Author(s): Buetow Lori | Brown Amanda | Parish Tanya | Hunter William
Volume: 7
Issue: 1
Year: 2007
Dimerization of inositol monophosphatase Mycobacterium tuberculosis SuhB is not constitutive, but induced by binding of the activator Mg2+

Author(s): Brown Alistair | Meng Guoyu | Ghadbane Hemza | Scott David | Dover Lynn | Nigou Jérôme | Besra Gurdyal | Fütterer Klaus
Volume: 7
Issue: 1
Year: 2007
Structural footprinting in protein structure comparison: the impact of structural fragments

Author(s): Zotenko Elena | Islamaj Dogan Rezarta | Wilbur W John | O'Leary Dianne | Przytycka Teresa
Volume: 7
Issue: 1
Year: 2007
The binding site for neohesperidin dihydrochalcone at the human sweet taste receptor

Author(s): Winnig Marcel | Bufe Bernd | Kratochwil Nicole | Slack Jay | Meyerhof Wolfgang
Volume: 7
Issue: 1
Year: 2007
Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases

Author(s): Ferraroni Marta | Myasoedova Nina | Schmatchenko Vadim | Leontievsky Alexey | Golovleva Ludmila | Scozzafava Andrea | Briganti Fabrizio
Volume: 7
Issue: 1
Year: 2007
Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails

Author(s): Huang Hongda | Zhang Jiahai | Shen Weiqun | Wang Xingsheng | Wu Jiawen | Wu Jihui | Shi Yunyu
Volume: 7
Issue: 1
Year: 2007
Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide

Author(s): Acharya Rudresh | Gupta Madhvi | Ramakumar Suryanarayanarao | Ramagopal Udupi | Chauhan Virander
Volume: 7
Issue: 1
Year: 2007
Spectrum of disease-causing mutations in protein secondary structures

Author(s): Khan Sofia | Vihinen Mauno
Volume: 7
Issue: 1
Year: 2007
Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development

Author(s): Parthiban Vijaya | Gromiha M Michael | Abhinandan Madenhalli | Schomburg Dietmar
Volume: 7
Issue: 1
Year: 2007
Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules

Author(s): Delatorre Plínio | Rocha Bruno | Souza Emmanuel | Oliveira Taianá | Bezerra Gustavo | Moreno Frederico | Freitas Beatriz | Santi-Gadelha Tatiane | Sampaio Alexandre | Azevedo Walter | Cavada Benildo
Volume: 7
Issue: 1
Year: 2007
Comparative Analysis of Protein Structure Alignments

Author(s): Mayr Gabriele | Domingues Francisco | Lackner Peter
Volume: 7
Issue: 1
Year: 2007
(NZ)CH...O Contacts assist crystallization of a ParB-like nuclease

Author(s): Shaw Neil | Cheng Chongyun | Tempel Wolfram | Chang Jessie | Ng Joseph | Wang Xin-Yu | Perrett Sarah | Rose John | Rao Zihe | Wang Bi-Cheng | Liu Zhi-Jie
Volume: 7
Issue: 1
Year: 2007
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily

Author(s): Ibryashkina Elena | Zakharova Marina | Baskunov Vladimir | Bogdanova Ekaterina | Nagornykh Maxim | Den'mukhamedov Marat | Melnik Bogdan | Kolinski Andrzej | Gront Dominik | Feder Marcin | Solonin Alexander | Bujnicki Janusz
Volume: 7
Issue: 1
Year: 2007
In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach

Author(s): Dell'Orco Daniele | De Benedetti Pier | Fanelli Francesca
Volume: 7
Issue: 1
Year: 2007
Differential scanning calorimetry study of glycerinated rabbit psoas muscle fibres in intermediate state of ATP hydrolysis

Author(s): Dergez Timea | Lőrinczy Dénes | Könczöl Franciska | Farkas Nelli | Belagyi Joseph
Volume: 7
Issue: 1
Year: 2007
Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1

Author(s): He Weiwei | Wang Yi | Liu Wei | Zhou Cong-Zhao
Volume: 7
Issue: 1
Year: 2007
X-ray structures of Na-GST-1 and Na-GST-2 two glutathione s-transferase from the human hookworm Necator americanus

Author(s): Asojo Oluwatoyin | Homma Kohei | Sedlacek Meghan | Ngamelue Michelle | Goud Gaddam | Zhan Bin | Deumic Vehid | Asojo Oluyomi | Hotez Peter
Volume: 7
Issue: 1
Year: 2007
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

Author(s): Kmiecik Sebastian | Gront Dominik | Kolinski Andrzej
Volume: 7
Issue: 1
Year: 2007
The role of hydrophobic interactions in positioning of peripheral proteins in membranes

Author(s): Lomize Andrei | Pogozheva Irina | Lomize Mikhail | Mosberg Henry
Volume: 7
Issue: 1
Year: 2007
Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

Author(s): Byun Jung-Sue | Rhee Jin-Kyu | Kim Nam | Yoon JeongHyeok | Kim Dong-Uk | Koh Eunhee | Oh Jong-Won | Cho Hyun-Soo
Volume: 7
Issue: 1
Year: 2007
Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly

Author(s): Schormann Norbert | Grigorian Alexei | Samal Alexandra | Krishnan Raman | DeLucas Lawrence | Chattopadhyay Debasish
Volume: 7
Issue: 1
Year: 2007
Engineering of PA-IIL lectin from Pseudomonas aeruginosa – Unravelling the role of the specificity loop for sugar preference

Author(s): Adam Jan | Pokorná Martina | Sabin Charles | Mitchell Edward | Imberty Anne | Wimmerová Michaela
Volume: 7
Issue: 1
Year: 2007
High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins

Author(s): Kim In-Kwon | Kim Min-Kyu | Kim Ji-Hye | Yim Hyung-Soon | Cha Sun-Shin | Kang Sa-Ouk
Volume: 7
Issue: 1
Year: 2007
The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family

Author(s): Burman Julia | Stevenson Clare | Sawers R Gary | Lawson David
Volume: 7
Issue: 1
Year: 2007
Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

Author(s): Ettrich Rüdiger | Kopecký Vladimír | Hofbauerová Kateřina | Baumruk Vladimír | Novák Petr | Pompach Petr | Man Petr | Plíhal Ondřej | Kutý Michal | Kulik Natallia | Sklenář Jan | Ryšlavá Helena | Křen Vladimír | Bezouška Karel
Volume: 7
Issue: 1
Year: 2007
Characterizing structural features of cuticle-degrading proteases from fungi by molecular modeling

Author(s): Liu Shu-Qun | Meng Zhao-Hui | Yang Jin-Kui | Fu Yun-Xin | Zhang Ke-Qin
Volume: 7
Issue: 1
Year: 2007
X-ray sequence and crystal structure of luffaculin 1, a novel type 1 ribosome-inactivating protein

Author(s): Hou Xiaomin | Chen Minghuang | Chen Liqing | Meehan Edward | Xie Jieming | Huang Mingdong
Volume: 7
Issue: 1
Year: 2007
Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

Author(s): Guvench Olgun | Qu Cheng-Kui | MacKerell Alexander
Volume: 7
Issue: 1
Year: 2007
Rappertk: a versatile engine for discrete restraint-based conformational sampling of macromolecules

Author(s): Gore Swanand | Karmali Anjum | Blundell Tom
Volume: 7
Issue: 1
Year: 2007
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1

Author(s): Ferraro Daniel | Brown Eric | Yu Chi-Li | Parales Rebecca | Gibson David | Ramaswamy S
Volume: 7
Issue: 1
Year: 2007
Structure, substrate recognition and reactivity of Leishmania major mevalonate kinase

Author(s): Sgraja Tanja | Smith Terry | Hunter William
Volume: 7
Issue: 1
Year: 2007
Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles

Author(s): Greaves Richard | Warwicker Jim
Volume: 7
Issue: 1
Year: 2007
Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling

Author(s): Rakhmanov Sergei | Makeev Vsevolod
Volume: 7
Issue: 1
Year: 2007
Binding of Sudan II and IV to lecithin liposomes and E. coli membranes: insights into the toxicity of hydrophobic azo dyes

Author(s): Li Lu | Gao Hong-Wen | Ren Jiao-Rong | Chen Ling | Li Yu-Cheng | Zhao Jian-Fu | Zhao He-Ping | Yuan Yuan
Volume: 7
Issue: 1
Year: 2007
Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

Author(s): Madej Thomas | Panchenko Anna | Chen Jie | Bryant Stephen
Volume: 7
Issue: 1
Year: 2007
The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3

Author(s): Casares Salvador | AB Eiso | Eshuis Henk | Lopez-Mayorga Obdulio | van Nuland Nico | Conejero-Lara Francisco
Volume: 7
Issue: 1
Year: 2007
A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding

Author(s): Stanley Will | Pursiainen Niko | Garman Elspeth | Juffer André | Wilmanns Matthias | Kursula Petri
Volume: 7
Issue: 1
Year: 2007
Scoring predictive models using a reduced representation of proteins: model and energy definition

Author(s): Fogolari Federico | Pieri Lidia | Dovier Agostino | Bortolussi Luca | Giugliarelli Gilberto | Corazza Alessandra | Esposito Gennaro | Viglino Paolo
Volume: 7
Issue: 1
Year: 2007
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect

Author(s): Jang Hyunbum | Ma Buyong | Nussinov Ruth
Volume: 7
Issue: 1
Year: 2007
Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

Author(s): Chen Ke | Kurgan Lukasz | Ruan Jishou
Volume: 7
Issue: 1
Year: 2007
Quaternary structure of Artemia haemoglobin II: analysis of T and C polymer alignment and interpolymer interface

Author(s): Chyou David | Rawle Vincent | Trotman Clive
Volume: 7
Issue: 1
Year: 2007
Evaluation of the structural quality of modeled proteins by using globularity criteria

Author(s): Costantini Susan | Facchiano Angelo | Colonna Giovanni
Volume: 7
Issue: 1
Year: 2007
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A)

Author(s): Hytönen Vesa | Määttä Juha | Niskanen Einari | Huuskonen Juhani | Helttunen Kaisa | Halling Katrin | Nordlund Henri | Rissanen Kari | Johnson Mark | Salminen Tiina | Kulomaa Markku | Laitinen Olli | Airenne Tomi
Volume: 7
Issue: 1
Year: 2007
Protein structure prediction by all-atom free-energy refinement

Author(s): Verma Abhinav | Wenzel Wolfgang
Volume: 7
Issue: 1
Year: 2007
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for α-keto acid binding

Author(s): Gonin Sophie | Arnoux Pascal | Pierru Bénédicte | Lavergne Jérôme | Alonso Béatrice | Sabaty Monique | Pignol David
Volume: 7
Issue: 1
Year: 2007
A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor

Author(s): Weber Dionys | Kotzsch Alexander | Nickel Joachim | Harth Stefan | Seher Axel | Mueller Uwe | Sebald Walter | Mueller Thomas
Volume: 7
Issue: 1
Year: 2007
Energetics of the protein-DNA-water interaction

Author(s): Spyrakis Francesca | Cozzini Pietro | Bertoli Chiara | Marabotti Anna | Kellogg Glen | Mozzarelli Andrea
Volume: 7
Issue: 1
Year: 2007
A generalized analysis of hydrophobic and loop clusters within globular protein sequences

Author(s): Eudes Richard | Le Tuan Khanh | Delettré Jean | Mornon Jean-Paul | Callebaut Isabelle
Volume: 7
Issue: 1
Year: 2007
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center

Author(s): Saikatendu Kumar | Zhang Xuejun | Kinch Lisa | Leybourne Matthew | Grishin Nick | Zhang Hong
Volume: 6
Issue: 1
Year: 2006
Analysis of an optimal hidden Markov model for secondary structure prediction

Author(s): Martin Juliette | Gibrat Jean-François | Rodolphe François
Volume: 6
Issue: 1
Year: 2006
Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics

Author(s): Antczak Andrew | Tsubota Toshiaki | Kaufman Paul | Berger James
Volume: 6
Issue: 1
Year: 2006
Autoinsertion of soluble oligomers of Alzheimer's Aβ(1–42) peptide into cholesterol-containing membranes is accompanied by relocation of the sterol towards the bilayer surface

Author(s): Ashley Richard | Harroun Thad | Hauss Thomas | Breen Kieran | Bradshaw Jeremy
Volume: 6
Issue: 1
Year: 2006
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU

Author(s): Saha Rudra | Chakrabarti Pinak
Volume: 6
Issue: 1
Year: 2006
Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design

Author(s): El Omari Kamel | Solaroli Nicola | Karlsson Anna | Balzarini Jan | Stammers David
Volume: 6
Issue: 1
Year: 2006
Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4–55 PHA synthase and an insight into its catalytic mechanism

Author(s): Wahab Habibah | Ahmad Khairudin Nurul | Samian Mohd | Najimudin Nazalan
Volume: 6
Issue: 1
Year: 2006
The crystal structure of superoxide dismutase from Plasmodium falciparum

Author(s): Boucher Ian | Brzozowski Andrzej | Brannigan James | Schnick Claudia | Smith Derek | Kyes Sue | Wilkinson Anthony
Volume: 6
Issue: 1
Year: 2006
Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy

Author(s): Kachel Norman | Kremer Werner | Zahn Ralph | Kalbitzer Hans
Volume: 6
Issue: 1
Year: 2006
A general method for the unbiased improvement of solution NMR structures by the use of related X-Ray data, the AUREMOL-ISIC algorithm

Author(s): Brunner Konrad | Gronwald Wolfram | Trenner Jochen | Neidig Klaus-Peter | Kalbitzer Hans
Volume: 6
Issue: 1
Year: 2006
Similar folds with different stabilization mechanisms: the cases of prion and doppel proteins

Author(s): Colacino Stefano | Tiana Guido | Colombo Giorgio
Volume: 6
Issue: 1
Year: 2006
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

Author(s): Chen Luonan | Wu Ling-Yun | Wang Yong | Zhang Shihua | Zhang Xiang-Sun
Volume: 6
Issue: 1
Year: 2006
Saturating representation of loop conformational fragments in structure databanks

Author(s): Fernandez-Fuentes Narcis | Fiser András
Volume: 6
Issue: 1
Year: 2006
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification

Author(s): Zotenko Elena | O'Leary Dianne | Przytycka Teresa
Volume: 6
Issue: 1
Year: 2006
Prediction of transmembrane helix orientation in polytopic membrane proteins

Author(s): Adamian Larisa | Liang Jie
Volume: 6
Issue: 1
Year: 2006
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces

Author(s): Saha Rudra | Bahadur Ranjit | Pal Arumay | Mandal Saptarshi | Chakrabarti Pinak
Volume: 6
Issue: 1
Year: 2006
Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications

Author(s): Chandonia John-Marc | Kim Sung-Hou
Volume: 6
Issue: 1
Year: 2006
Fold classification based on secondary structure – how much is gained by including loop topology?

Author(s): Jeong Jieun | Berman Piotr | Przytycka Teresa
Volume: 6
Issue: 1
Year: 2006
Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Author(s): Davies Matthew | Hattotuwagama Channa | Moss David | Drew Michael | Flower Darren
Volume: 6
Issue: 1
Year: 2006
Identification of similar regions of protein structures using integrated sequence and structure analysis tools

Author(s): Peters Brandon | Moad Charles | Youn Eunseog | Buffington Kris | Heiland Randy | Mooney Sean
Volume: 6
Issue: 1
Year: 2006
Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium

Author(s): Argiriadi Maria | Goedken Eric | Bruck Irina | O'Donnell Mike | Kuriyan John
Volume: 6
Issue: 1
Year: 2006
DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways

Author(s): Pugh David | AB Eiso | Faro Andrew | Lutya Portia | Hoffmann Eberhard | Rees D Jasper
Volume: 6
Issue: 1
Year: 2006
X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1)

Author(s): Manjasetty Babu | Niesen Frank | Scheich Christoph | Roske Yvette | Goetz Frank | Behlke Joachim | Sievert Volker | Heinemann Udo | Büssow Konrad
Volume: 5
Issue: 1
Year: 2005
Natural history of S-adenosylmethionine-binding proteins

Author(s): Kozbial Piotr | Mushegian Arcady
Volume: 5
Issue: 1
Year: 2005
Prediction of "hot spots" of aggregation in disease-linked polypeptides

Author(s): de Groot Natalia | Pallarés Irantzu | Avilés Francesc | Vendrell Josep | Ventura Salvador
Volume: 5
Issue: 1
Year: 2005
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

Author(s): Martin Juliette | Letellier Guillaume | Marin Antoine | Taly Jean-François | de Brevern Alexandre | Gibrat Jean-François
Volume: 5
Issue: 1
Year: 2005
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different

Author(s): De Subhajyoti | Krishnadev O | Srinivasan N | Rekha N
Volume: 5
Issue: 1
Year: 2005
Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis

Author(s): Ren Jingshan | Sainsbury Sarah | Berrow Nick | Alderton David | Nettleship Joanne | Stammers David | Saunders Nigel | Owens Raymond
Volume: 5
Issue: 1
Year: 2005
A model of the ternary complex of interleukin-10 with its soluble receptors

Author(s): Pletnev Sergei | Magracheva Eugenia | Wlodawer Alexander | Zdanov Alexander
Volume: 5
Issue: 1
Year: 2005
Structural organization and interactions of transmembrane domains in tetraspanin proteins

Author(s): Kovalenko Oleg | Metcalf Douglas | DeGrado William | Hemler Martin
Volume: 5
Issue: 1
Year: 2005
Nh3D: A reference dataset of non-homologous protein structures

Author(s): Thiruv B | Quon G | Saldanha SA | Steipe B
Volume: 5
Issue: 1
Year: 2005
2Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Author(s): Pahlke Doreen | Freund Christian | Leitner Dietmar | Labudde Dirk
Volume: 5
Issue: 1
Year: 2005
Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold

Author(s): Roßbach Michael | Daumke Oliver | Klinger Claudia | Wittinghofer Alfred | Kaufmann Michael
Volume: 5
Issue: 1
Year: 2005
A comprehensive update of the sequence and structure classification of kinases

Author(s): Cheek Sara | Ginalski Krzysztof | Zhang Hong | Grishin Nick
Volume: 5
Issue: 1
Year: 2005
Cα-H···O = C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

Author(s): Bella Jordi | Humphries Martin
Volume: 5
Issue: 1
Year: 2005
Deciphering structure and topology of conserved COG2042 orphan proteins

Author(s): Armengaud Jean | Dedieu Alain | Solques Olivier | Pellequer Jean-Luc | Quemeneur Eric
Volume: 5
Issue: 1
Year: 2005
A homology model of restriction endonuclease SfiI in complex with DNA

Author(s): Chmiel Agnieszka | Bujnicki Janusz | Skowronek Krzysztof
Volume: 5
Issue: 1
Year: 2005
Molecular models of NS3 protease variants of the Hepatitis C virus

Author(s): da Silveira Nelson | Arcuri Helen | Bonalumi Carlos | de Souza Fátima | Mello Isabel | Rahal Paula | Pinho João | de Azevedo Walter
Volume: 5
Issue: 1
Year: 2005
Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

Author(s): Wernimont Amy | Weissenhorn Winfried
Volume: 4
Issue: 1
Year: 2004
Improved protein structure selection using decoy-dependent discriminatory functions

Author(s): Wang Kai | Fain Boris | Levitt Michael | Samudrala Ram
Volume: 4
Issue: 1
Year: 2004
Ionic self-complementarity induces amyloid-like fibril formation in an isolated domain of a plant copper metallochaperone protein

Author(s): Mira Helena | Vilar Marçal | Esteve Vicent | Martinell Marc | Kogan Marcelo | Giralt Ernest | Salom David | Mingarro Ismael | Peñarrubia Lola | Pérez-Payá Enrique
Volume: 4
Issue: 1
Year: 2004
Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

Author(s): Scheich Christoph | Leitner Dietmar | Sievert Volker | Leidert Martina | Schlegel Brigitte | Simon Bernd | Letunic Ivica | Büssow Konrad | Diehl Anne
Volume: 4
Issue: 1
Year: 2004
COMe: the ontology of bioinorganic proteins

Author(s): Degtyarenko Kirill | Contrino Sergio
Volume: 4
Issue: 1
Year: 2004
Collagenolytic serine protease PC and trypsin PC from king crab Paralithodes camtschaticus: cDNA cloning and primary structure of the enzymes

Author(s): Rudenskaya Galina | Kislitsin Yuri | Rebrikov Denis
Volume: 4
Issue: 1
Year: 2004
A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases

Author(s): Wlodawer Alexander | Durell Stewart | Li Mi | Oyama Hiroshi | Oda Kohei | Dunn Ben
Volume: 3
Issue: 1
Year: 2003
Crystal structural analysis of human serum albumin complexed with hemin and fatty acid

Author(s): Zunszain Patricia | Ghuman Jamie | Komatsu Teruyuki | Tsuchida Eishun | Curry Stephen
Volume: 3
Issue: 1
Year: 2003
Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

Author(s): Hughes Samantha | Tanner Julian | Hindley Alison | Miller Andrew | Gould Ian
Volume: 3
Issue: 1
Year: 2003
Tripeptide analysis of protein structures

Author(s): Anishetty Sharmila | Pennathur Gautam | Anishetty Ramesh
Volume: 2
Issue: 1
Year: 2002
Structural analysis of hemicatenated DNA loops

Author(s): Gaillard Claire | Shlyakhtenko Luda | Lyubchenko Yuri | Strauss François
Volume: 2
Issue: 1
Year: 2002
Crystal structure of LIR-2 (ILT4) at 1.8 Å: differences from LIR-1 (ILT2) in regions implicated in the binding of the Human Cytomegalovirus class I MHC homolog UL18

Author(s): Willcox Benjamin | Thomas Leonard | Chapman Tara | Heikema Astrid | West Anthony | Bjorkman Pamela
Volume: 2
Issue: 1
Year: 2002
Native interface of the SAM domain polymer of TEL

Author(s): Tran Hoang | Kim Chongwoo | Faham Salem | Siddall Marie-Claire | Bowie James
Volume: 2
Issue: 1
Year: 2002
A protein folding potential that places the native states of a large number of proteins near a local minimum

Author(s): Chhajer Mukesh | Crippen Gordon
Volume: 2
Issue: 1
Year: 2002
A comprehensive analysis of 40 blind protein structure predictions

Author(s): Samudrala Ram | Levitt Michael
Volume: 2
Issue: 1
Year: 2002
Types of inter-atomic interactions at the MHC-peptide interface: Identifying commonality from accumulated data

Author(s): Adrian Png | Rajaseger Ganapathy | Mathura Venkatarajan | Sakharkar Meena | Kangueane Pandjassarame
Volume: 2
Issue: 1
Year: 2002
Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

Author(s): Schapira Matthieu | Abagyan Ruben | Totrov Maxim
Volume: 2
Issue: 1
Year: 2002
Functional evolution of two subtly different (similar) folds

Author(s): Agrawal Vishal | Kishan Radha
Volume: 1
Issue: 1
Year: 2001
Insight to structural subsite recognition in plant thiol protease-inhibitor complexes : Understanding the basis of differential inhibition and the role of water

Author(s): Bhattacharya Suparna | Ghosh Sreya | Chakraborty Sibani | Bera Asim | Mukhopadhayay Bishnu | Dey Indrani | Banerjee Asok
Volume: 1
Issue: 1
Year: 2001
A geometric and algebraic view of MHC-peptide complexes and their binding properties

Author(s): Cano Pedro | Fan Bo
Volume: 1
Issue: 1
Year: 2001
Human Nek6 is a monomeric mostly globular kinase with an unfolded short N-terminal domain

Author(s): Meirelles Gabriela | Silva Júlio | Mendonça Yuri | Ramos Carlos | Torriani Iris | Kobarg Jörg
Volume: 11
Issue: 1
Year: 2011
Structural analysis of heme proteins: implications for design and prediction

Author(s): Li Ting | Bonkovsky Herbert | Guo Jun-tao
Volume: 11
Issue: 1
Year: 2011
Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin

Author(s): Arenas Nelson | Salazar Luz | Soto Carlos | Vizcaíno Carolina | Patarroyo Manuel | Patarroyo Manuel | Gómez Arley
Volume: 11
Issue: 1
Year: 2011
Structural studies of the mechanism for biosensing antibiotics in a fluorescein-labeled β-lactamase

Author(s): Wong Wai-Ting | Au Ho-Wah | Yap Hong-Kin | Leung Yun-Chung | Wong Kwok-Yin | Zhao Yanxiang
Volume: 11
Issue: 1
Year: 2011
Designing coarse grained-and atom based-potentials for protein-protein docking

Author(s): Tobi Dror
Volume: 10
Issue: 1
Year: 2010
Modulation of inhibitory activity of xylanase - α-amylase inhibitor protein (XAIP): binding studies and crystal structure determination of XAIP- II from Scadoxus multiflorus at 1.2 Å resolution

Author(s): Kumar Sanjit | Singh Nagendra | Mishra Biswajit | Dube Divya | Sinha Mau | Singh S Baskar | Dey Sharmistha | Kaur Punit | Sharma Sujata | Singh Tej
Volume: 10
Issue: 1
Year: 2010
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes

Author(s): Torella Rubben | Moroni Elisabetta | Caselle Michele | Morra Giulia | Colombo Giorgio
Volume: 10
Issue: 1
Year: 2010
Structural insights into the membrane-extracted dimeric form of the ATPase TraB from the Escherichia coli pKM101 conjugation system

Author(s): Durand Eric | Waksman Gabriel | Receveur-Brechot Veronique
Volume: 11
Issue: 1
Year: 2011
In Silico Quantitative Structure-Activity Relationship Studies on P-gp Modulators of Tetrahydroisoquinoline-Ethyl-Phenylamine Series

Author(s): Gadhe Changdev | Madhavan Thirumurthy | Kothandan Gugan | Cho Seung
Volume: 11
Issue: 1
Year: 2011
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

Author(s): Rostkowski Michał | Olsson Mats | Søndergaard Chresten | Jensen Jan
Volume: 11
Issue: 1
Year: 2011
Differential molecular information of maurotoxin peptide recognizing IKCa and Kv1.2 channels explored by computational simulation

Author(s): Yi Hong | Qiu Su | Wu Yingliang | Li Wenxin | Wang Baoshan
Volume: 11
Issue: 1
Year: 2011
Deciphering the shape and deformation of secondary structures through local conformation analysis

Author(s): Baussand Julie | Camproux Anne-Claude
Volume: 11
Issue: 1
Year: 2011
DeStripe: frequency-based algorithm for removing stripe noises from AFM images

Author(s): Chen Shu-wen | Pellequer Jean-Luc
Volume: 11
Issue: 1
Year: 2011
Inositol pentakisphosphate isomers bind PH domains with varying specificity and inhibit phosphoinositide interactions

Author(s): Jackson Sean | Al-Saigh Sarra | Schultz Carsten | Junop Murray
Volume: 11
Issue: 1
Year: 2011
Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

Author(s): Ahmad Shandar | Sarai Akinori
Volume: 11
Issue: 1
Year: 2011
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors

Author(s): Ribeiro Cristina | Togawa Roberto | Neshich Izabella | Mazoni Ivan | Mancini Adauto | Minardi Raquel | da Silveira Carlos | Jardine José | Santoro Marcelo | Neshich Goran
Volume: 10
Issue: 1
Year: 2010
Investigation and improvement of DNA cleavage models of polyamide + Cu(II) nuclease + OOH- ligands bound to DNA

Author(s): Yue Hongwei | Zhu Yanyan | Wang Yan | Chen Guangju
Volume: 10
Issue: 1
Year: 2010
DockAnalyse: an application for the analysis of protein-protein interactions

Author(s): Amela Isaac | Delicado Pedro | Gómez Antonio | Bonàs Sílvia | Querol Enrique | Cedano Juan
Volume: 10
Issue: 1
Year: 2010
The intriguing Cyclophilin A-HIV-1 Vpr interaction: prolyl cis/trans isomerisation catalysis and specific binding

Author(s): Solbak Sara | Reksten Tove | Wray Victor | Bruns Karsten | Horvli Ole | Raae Arnt | Henklein Petra | Henklein Peter | Röder Rene | Mitzner David | Schubert Ulrich | Fossen Torgils
Volume: 10
Issue: 1
Year: 2010
Molecular determinants of improved cathepsin B inhibition by new cystatins obtained by DNA shuffling

Author(s): Valadares Napoleão | Dellamano Márcia | Soares-Costa Andrea | Henrique-Silva Flávio | Garratt Richard
Volume: 10
Issue: 1
Year: 2010
A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis

Author(s): Guo Qinglan | Weng Jingwei | Xu Xiaogang | Wang Minghua | Wang Xiaoying | Ye Xinyu | Wang Wenning | Wang Minggui
Volume: 10
Issue: 1
Year: 2010
Prediction and analysis of the modular structure of cytochrome P450 monooxygenases

Author(s): Sirim Demet | Widmann Michael | Wagner Florian | Pleiss Jürgen
Volume: 10
Issue: 1
Year: 2010
Relating the shape of protein binding sites to binding affinity profiles: is there an association?

Author(s): Simon Zoltán | Vigh-Smeller Margit | Peragovics Ágnes | Csukly Gábor | Zahoránszky-Kőhalmi Gergely | Rauscher Anna | Jelinek Balázs | Hári Péter | Bitter István | Málnási-Csizmadia András | Czobor Pál
Volume: 10
Issue: 1
Year: 2010
Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone

Author(s): Barta Michael | Zhang Lingling | Picking Wendy | Geisbrecht Brian
Volume: 10
Issue: 1
Year: 2010
Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

Author(s): Li Yaohang | Rata Ionel | Chiu See-wing | Jakobsson Eric
Volume: 10
Issue: 1
Year: 2010
Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

Author(s): Hirose Shuichi | Yokota Kiyonobu | Kuroda Yutaka | Wako Hiroshi | Endo Shigeru | Kanai Satoru | Noguchi Tamotsu
Volume: 10
Issue: 1
Year: 2010
Systematic analysis of short internal indels and their impact on protein folding

Author(s): Kim RyangGuk | Guo Jun-tao
Volume: 10
Issue: 1
Year: 2010
Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

Author(s): Doxey Andrew | Cheng Zhenyu | Moffatt Barbara | McConkey Brendan
Volume: 10
Issue: 1
Year: 2010
Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains

Author(s): Bird Louise | Ren Jingshan | Nettleship Joanne | Folkers Gert | Owens Raymond | Stammers David
Volume: 10
Issue: 1
Year: 2010
Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase

Author(s): Soisson Stephen | Patel Sangita | Abeywickrema Pravien | Byrne Noel | Diehl Ronald | Hall Dawn | Ford Rachael | Reid John | Rickert Keith | Shipman Jennifer | Sharma Sujata | Lumb Kevin
Volume: 10
Issue: 1
Year: 2010
Solution structure of the human signaling protein RACK1

Author(s): Gonçalves Kaliandra | Borges Julio | Silva Julio | Papa Priscila | Bressan Gustavo | Torriani Iris | Kobarg Jörg
Volume: 10
Issue: 1
Year: 2010
Novel topological descriptors for analyzing biological networks

Author(s): Dehmer Matthias | Barbarini Nicola | Varmuza Kurt | Graber Armin
Volume: 10
Issue: 1
Year: 2010
Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Author(s): Gadkari Rupali | Srinivasan Narayanaswamy
Volume: 10
Issue: 1
Year: 2010
A kinesin motor in a force-producing conformation

Author(s): Heuston Elisabeth | Bronner C Eric | Kull F Jon | Endow Sharyn
Volume: 10
Issue: 1
Year: 2010
The structure of a reduced form of OxyR from Neisseria meningitidis

Author(s): Sainsbury Sarah | Ren Jingshan | Nettleship Joanne | Saunders Nigel | Stuart David | Owens Raymond
Volume: 10
Issue: 1
Year: 2010
Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach

Author(s): Parravicini Chiara | Abbracchio Maria | Fantucci Piercarlo | Ranghino Graziella
Volume: 10
Issue: 1
Year: 2010
Prediction of calcium-binding sites by combining loop-modeling with machine learning

Author(s): Liu Tianyun | Altman Russ
Volume: 9
Issue: 1
Year: 2009
Analysis of the role of PCNA-DNA contacts during clamp loading

Author(s): McNally Randall | Bowman Gregory | Goedken Eric | O'Donnell Mike | Kuriyan John
Volume: 10
Issue: 1
Year: 2010
Crystal structure of the signaling helix coiled-coil domain of the β1 subunit of the soluble guanylyl cyclase

Author(s): Ma Xiaolei | Beuve Annie | van den Akker Focco
Volume: 10
Issue: 1
Year: 2010
Modeling of loops in proteins: a multi-method approach

Author(s): Jamroz Michal | Kolinski Andrzej
Volume: 10
Issue: 1
Year: 2010
Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein

Author(s): Sharma Alok | Bruns Karsten | Röder René | Henklein Peter | Votteler Jörg | Wray Victor | Schubert Ulrich
Volume: 9
Issue: 1
Year: 2009
The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes

Author(s): Chang Changsoo | Coggill Penny | Bateman Alex | Finn Robert | Cymborowski Marcin | Otwinowski Zbyszek | Minor Wladek | Volkart Lour | Joachimiak Andrzej
Volume: 9
Issue: 1
Year: 2009
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

Author(s): Özen Ayşegül | Gönen Mehmet | Alpaydın Ethem | Haliloğlu Türkan
Volume: 9
Issue: 1
Year: 2009
Molecular models for intrastrand DNA G-quadruplexes

Author(s): Fogolari Federico | Haridas Haritha | Corazza Alessandra | Viglino Paolo | Corà Davide | Caselle Michele | Esposito Gennaro | Xodo Luigi
Volume: 9
Issue: 1
Year: 2009
Conformational changes and loose packing promote E. coli Tryptophanase cold lability

Author(s): Kogan Anna | Gdalevsky Garik | Cohen-Luria Rivka | Goldgur Yehuda | Phillips Robert | Parola Abraham | Almog Orna
Volume: 9
Issue: 1
Year: 2009
Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Author(s): Stocks Matthew | Hayward Steven | Laycock Stephen
Volume: 9
Issue: 1
Year: 2009
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103

Author(s): Teng Yan-Bin | Jiang Yong-Liang | He Yong-Xing | He Wei-Wei | Lian Fu-Ming | Chen Yuxing | Zhou Cong-Zhao
Volume: 9
Issue: 1
Year: 2009
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography

Author(s): Lakomek Kristina | Dickmanns Achim | Kettwig Matthias | Urlaub Henning | Ficner Ralf | Lübke Torben
Volume: 9
Issue: 1
Year: 2009
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)

Author(s): Couñago Rafael | Davlieva Milya | Strych Ulrich | Hill Ryan | Krause Kurt
Volume: 9
Issue: 1
Year: 2009
Low-resolution structural studies of human Stanniocalcin-1

Author(s): Trindade Daniel | Silva Júlio | Navarro Margareth | Torriani Iris | Kobarg Jörg
Volume: 9
Issue: 1
Year: 2009
Exploring protein structural dissimilarity to facilitate structure classification

Author(s): Jain Pooja | Hirst Jonathan
Volume: 9
Issue: 1
Year: 2009
Mirrors in the PDB: left-handed α-turns guide design with D-amino acids

Author(s): Annavarapu Srinivas | Nanda Vikas
Volume: 9
Issue: 1
Year: 2009
Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor

Author(s): Veljkovic Veljko | Niman Henry | Glisic Sanja | Veljkovic Nevena | Perovic Vladimir | Muller Claude
Volume: 9
Issue: 1
Year: 2009
Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases

Author(s): Chaikuad Apirat | Brady R Leo
Volume: 9
Issue: 1
Year: 2009
A generic method for assignment of reliability scores applied to solvent accessibility predictions

Author(s): Petersen Bent | Petersen Thomas | Andersen Pernille | Nielsen Morten | Lundegaard Claus
Volume: 9
Issue: 1
Year: 2009
CRYSTALP2: sequence-based protein crystallization propensity prediction

Author(s): Kurgan Lukasz | Razib Ali | Aghakhani Sara | Dick Scott | Mizianty Marcin | Jahandideh Samad
Volume: 9
Issue: 1
Year: 2009
A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process

Author(s): Bruni Roberto | Costantino Angela | Tritarelli Elena | Marcantonio Cinzia | Ciccozzi Massimo | Rapicetta Maria | El Sawaf Gamal | Giuliani Alessandro | Ciccaglione Anna
Volume: 9
Issue: 1
Year: 2009
The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain

Author(s): Marbouty Martial | Saguez Cyril | Chauvat Franck
Volume: 9
Issue: 1
Year: 2009
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation

Author(s): Winter Jody | Christofi Panayiotis | Morroll Shaun | Bunting Karen
Volume: 9
Issue: 1
Year: 2009
Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor

Author(s): Gao Beile | Sugiman-Marangos Seiji | Junop Murray | Gupta Radhey
Volume: 9
Issue: 1
Year: 2009
Amyloidogenic determinants are usually not buried

Author(s): Frousios Kimon | Iconomidou Vassiliki | Karletidi Carolina-Maria | Hamodrakas Stavros
Volume: 9
Issue: 1
Year: 2009
Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra

Author(s): Sorzano Carlos | Otero Abraham | Olmos Estefanía | Carazo José
Volume: 9
Issue: 1
Year: 2009
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor

Author(s): Fang Yi | Liu Yu-Shen | Ramani Karthik
Volume: 9
Issue: 1
Year: 2009
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

Author(s): Fukuchi Satoshi | Homma Keiichi | Minezaki Yoshiaki | Gojobori Takashi | Nishikawa Ken
Volume: 9
Issue: 1
Year: 2009
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

Author(s): Marathe Arvind | Karandur Deepti | Bansal Manju
Volume: 9
Issue: 1
Year: 2009
Interaction of perfluorooctanoic acid with human serum albumin

Author(s): Wu Ling-Ling | Gao Hong-Wen | Gao Nai-Yun | Chen Fang-Fang | Chen Ling
Volume: 9
Issue: 1
Year: 2009
Improving consensus contact prediction via server correlation reduction

Author(s): Gao Xin | Bu Dongbo | Xu Jinbo | Li Ming
Volume: 9
Issue: 1
Year: 2009
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

Author(s): Andrabi Munazah | Mizuguchi Kenji | Sarai Akinori | Ahmad Shandar
Volume: 9
Issue: 1
Year: 2009
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins

Author(s): Ito Jun-ichi | Sonobe Yuki | Ikeda Kazuyoshi | Tomii Kentaro | Higo Junichi
Volume: 9
Issue: 1
Year: 2009
Improving protein structure similarity searches using domain boundaries based on conserved sequence information

Author(s): Thompson Kenneth | Wang Yanli | Madej Tom | Bryant Stephen
Volume: 9
Issue: 1
Year: 2009
Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

Author(s): Trodler Peter | Schmid Rolf | Pleiss Jürgen
Volume: 9
Issue: 1
Year: 2009
On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF

Author(s): Zheng Meiying | Cierpicki Tomasz | Momotani Ko | Artamonov Mykhaylo | Derewenda Urszula | Bushweller John | Somlyo Avril | Derewenda Zygmunt
Volume: 9
Issue: 1
Year: 2009
Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein

Author(s): Ng C Leong | Waterman David | Koonin Eugene | Walters Alison | Chong James | Isupov Michail | Lebedev Andrey | Bunka David | Stockley Peter | Ortiz-Lombardía Miguel | Antson Alfred
Volume: 9
Issue: 1
Year: 2009
Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

Author(s): Juhl P Benjamin | Trodler Peter | Tyagi Sadhna | Pleiss Jürgen
Volume: 9
Issue: 1
Year: 2009
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information

Author(s): Benkert Pascal | Schwede Torsten | Tosatto Silvio
Volume: 9
Issue: 1
Year: 2009
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

Author(s): Heikkinen Outi | Seppala Raili | Tossavainen Helena | Heikkinen Sami | Koskela Harri | Permi Perttu | Kilpeläinen Ilkka
Volume: 9
Issue: 1
Year: 2009
Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study

Author(s): Argiriadi Maria | Sousa Silvino | Banach David | Marcotte Douglas | Xiang Tao | Tomlinson Medha | Demers Megan | Harris Christopher | Kwak Silvia | Hardman Jennifer | Pietras Margaret | Quinn Lisa | DiMauro Jennifer | Ni Baofu | Mankovich John | Borhani David | Talanian Robert | Sadhukhan Ramkrishna
Volume: 9
Issue: 1
Year: 2009
Analysing the origin of long-range interactions in proteins using lattice models

Author(s): Noivirt-Brik Orly | Unger Ron | Horovitz Amnon
Volume: 9
Issue: 1
Year: 2009
ProteinShader: illustrative rendering of macromolecules

Author(s): Weber Joseph
Volume: 9
Issue: 1
Year: 2009
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