Citations (137)
Keep up to date with the latest research on this topic with citation updates for this article.
Read on this site (3)
Matteo De March, Giulia Di Rocco, Neal Hickey & Silvano Geremia. (2015) High-resolution crystal structure of the recombinant diheme cytochrome c from Shewanella baltica (OS155). Journal of Biomolecular Structure and Dynamics 33:2, pages 395-403.
Read now
Read now
Prasun Kumar & Manju Bansal. (2012) HELANAL-Plus: a web server for analysis of helix geometry in protein structures. Journal of Biomolecular Structure and Dynamics 30:6, pages 773-783.
Read now
Read now
Daniel Caballero-Rivera, Omar A. Cruz-Nieves, Jessica Oyola-Cintrón, David A. Torres-Nunez, Jose D. Otero-Cruz & José A. Lasalde-Dominicci. (2012) Tryptophan scanning mutagenesis reveals distortions in the helical structure of the δM4 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor. Channels 6:2, pages 111-123.
Read now
Read now
Articles from other publishers (134)
Farha Khan, Matthias Elgeti, Samuel Grandfield, Aviv Paz, Fiona B. Naughton, Frank V. Marcoline, Thorsten Althoff, Natalia Ermolova, Ernest M. Wright, Wayne L. Hubbell, Michael Grabe & Jeff Abramson. (2023) Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT. Nature Communications 14:1.
Crossref
Crossref
Erik Walinda, Kenji Sugase, Naoki Ishii, Masahiro Shirakawa, Kazuhiro Iwai & Daichi Morimoto. (2023) Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity. Journal of Biological Chemistry 299:9, pages 105165.
Crossref
Crossref
Arjun Sharma, Andriy Anishkin, Sergei Sukharev & Juan M. Vanegas. (2023) Tight hydrophobic core and flexible helices yield MscL with a high tension gating threshold and a membrane area mechanical strain buffer. Frontiers in Chemistry 11.
Crossref
Crossref
Alexandre G. de Brevern. (2023) An agnostic analysis of the human AlphaFold2 proteome using local protein conformations. Biochimie 207, pages 11-19.
Crossref
Crossref
J. Karl Spinti, Fernando Neiva Nunes & Manuel N. Melo. (2023) Room for improvement in the initial martini 3 parameterization of peptide interactions. Chemical Physics Letters, pages 140436.
Crossref
Crossref
Andrea Pasquadibisceglie, Virginia Quadrotta & Fabio Polticelli. (2023) In Silico Analysis of the Structural Dynamics and Substrate Recognition Determinants of the Human Mitochondrial Carnitine/Acylcarnitine SLC25A20 Transporter. International Journal of Molecular Sciences 24:4, pages 3946.
Crossref
Crossref
Tingting Zhao, Nischal Karki, Brian D. Zoltowski & Devin A. Matthews. (2022) Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant. PLOS Computational Biology 18:12, pages e1010794.
Crossref
Crossref
Shadi Fuladi, Sarah McGuinness & Fatemeh Khalili-Araghi. (2022) Role of TM3 in claudin-15 strand flexibility: A molecular dynamics study. Frontiers in Molecular Biosciences 9.
Crossref
Crossref
Hanna Baltrukevich & Sabina Podlewska. (2022) From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output. Frontiers in Pharmacology 13.
Crossref
Crossref
Ashok R Nayak & Montserrat Samsó. (2022) Ca2+ inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. eLife 11.
Crossref
Crossref
Pancham Lal Gupta, Justin S. Smith & Adrian E. Roitberg. (2021)
pH Effects and Cooperativity among Key Titratable Residues for
Escherichia coli
Glycinamide Ribonucleotide Transformylase
. The Journal of Physical Chemistry B 125:32, pages 9168-9185.
Crossref
Crossref
Daniela Glatzová, Harsha Mavila, Maria Chiara Saija, Tomáš Chum, Lukasz Cwiklik, Tomáš Brdička & Marek Cebecauer. (2021) The role of prolines and glycine in the transmembrane domain of LAT. The FEBS Journal 288:13, pages 4039-4052.
Crossref
Crossref
Krzysztof Szczepaniak, Adriana Bukala, Antonio Marinho da Silva Neto, Jan Ludwiczak & Stanislaw Dunin-Horkawicz. (2020) A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics 36:22-23, pages 5368-5376.
Crossref
Crossref
B. Vollmer, V. Pražák, D. VasishtanE. E. Jefferys, A. Hernandez-DuranM. Vallbracht, B. G. KluppT. C. MettenleiterM. Backovic, F. A. Rey, M. Topf & K. Grünewald. (2020) The prefusion structure of herpes simplex virus glycoprotein B. Science Advances 6:39.
Crossref
Crossref
Ezequiel N. Frigini, Exequiel E. Barrera, Sergio Pantano & Rodolfo D. Porasso. (2020) Role of membrane curvature on the activation/deactivation of Carnitine Palmitoyltransferase 1A: A coarse grain molecular dynamic study. Biochimica et Biophysica Acta (BBA) - Biomembranes 1862:2, pages 183094.
Crossref
Crossref
Urška Slapšak, Giulia Salzano, Gregor Ilc, Gabriele Giachin, Jifeng Bian, Glenn Telling, Giuseppe Legname & Janez Plavec. (2019) Unique Structural Features of Mule Deer Prion Protein Provide Insights into Chronic Wasting Disease. ACS Omega 4:22, pages 19913-19924.
Crossref
Crossref
Shu Li, Bohua Wu & Wei Han. (2019) Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins. The Journal of Physical Chemistry B 123:10, pages 2254-2269.
Crossref
Crossref
Aditya Kumar Sarkar & Ansuman Lahiri. (2019) Dynamical Features of Cognate Site Recognition in bZIP–DNA Interaction. ACS Omega 4:1, pages 292-308.
Crossref
Crossref
Sandeep Kaushik & Soumya Lipsa Rath. 2019. Encyclopedia of Bioinformatics and Computational Biology. Encyclopedia of Bioinformatics and Computational Biology
520
538
.
Ammu P. Kumar, Suryani Lukman & Minh N. Nguyen. 2019. Encyclopedia of Bioinformatics and Computational Biology. Encyclopedia of Bioinformatics and Computational Biology
780
791
.
Prasun Kumar, Swagata Halder & Manju Bansal. 2019. Encyclopedia of Bioinformatics and Computational Biology. Encyclopedia of Bioinformatics and Computational Biology
504
534
.
Mai F. Alfahad, John T. Kent & Kanti V. Mardia. (2018) Statistical Shape Methodology for the Analysis of Helices. Sankhya A 80:S1, pages 8-32.
Crossref
Crossref
Marina A. Kasimova, Aysenur Torun Yazici, Yevgen Yudin, Daniele Granata, Michael L. Klein, Tibor Rohacs & Vincenzo Carnevale. (2018) A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine. Journal of General Physiology 150:11, pages 1554-1566.
Crossref
Crossref
Kanti V. Mardia, Karthik Sriram & Charlotte M. Deane. (2018) A statistical model for helices with applications. Biometrics 74:3, pages 845-854.
Crossref
Crossref
Shuangyu Bi, Fan Jin & Victor Sourjik. (2018) Inverted signaling by bacterial chemotaxis receptors. Nature Communications 9:1.
Crossref
Crossref
Renate Gessmann, Hans Brückner, Albrecht Berg & Kyriacos Petratos. (2018)
The crystal structure of the lipoaminopeptaibol helioferin, an antibiotic peptide from
Mycogone rosea
. Acta Crystallographica Section D Structural Biology 74:4, pages 315-320.
Crossref
Crossref
Leah Cairns, Thao Tran, Brendan H. Fowl, Angela Patterson, Yoo Jin Kim, Brian Bothner & Jennifer M. Kavran. (2018) Salvador has an extended SARAH domain that mediates binding to Hippo kinase. Journal of Biological Chemistry 293:15, pages 5532-5543.
Crossref
Crossref
Georgina Csizmadia, Bianka Farkas, Zoltán Spagina, Hedvig Tordai & Tamás Hegedűs. (2018) Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way. Computational and Structural Biotechnology Journal 16, pages 396-403.
Crossref
Crossref
Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, John H. Morris & Thomas E. Ferrin. (2017) UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science 27:1, pages 14-25.
Crossref
Crossref
Jens M. H. Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang & Daniel J. Rigden. (2017)
Approaches to
ab initio
molecular replacement of α-helical transmembrane proteins
. Acta Crystallographica Section D Structural Biology 73:12, pages 985-996.
Crossref
Crossref
Angana Ray, Navjeet Ahalawat & Jagannath Mondal. (2017) Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E. Biophysical Journal 113:12, pages 2682-2694.
Crossref
Crossref
Suk-Jun Youn, Na-Young Kwon, Ji Hyun Lee, Jin Hong Kim, Jinwoo Choi, Hayyoung Lee & Jie-Oh Lee. (2017) Construction of novel repeat proteins with rigid and predictable structures using a shared helix method. Scientific Reports 7:1.
Crossref
Crossref
Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling & Evangelos Coutsias. (2017) Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. Journal of Chemical Information and Modeling 57:4, pages 864-874.
Crossref
Crossref
Tarun Jairaj Narwani, Hubert Santuz, Nicolas Shinada, Akhila Melarkode Vattekatte, Yassine Ghouzam, Narayanasamy Srinivasan, Jean-Christophe Gelly & Alexandre G. de Brevern. (2017) Recent advances on polyproline II. Amino Acids 49:4, pages 705-713.
Crossref
Crossref
Tsung-Wei Su, Chao-Yu Yang, Wen-Pin Kao, Bai-Jiun Kuo, Shan-Meng Lin, Jung-Yaw Lin, Yu-Chih Lo & Su-Chang Lin. (2017) Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome. Structure 25:3, pages 407-420.
Crossref
Crossref
Renate Gessmann, Danny Axford, Hans Brückner, Albrecht Berg & Kyriacos Petratos. (2017) A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution. Acta Crystallographica Section F Structural Biology Communications 73:2, pages 95-100.
Crossref
Crossref
Shan-Meng Lin, Su-Chang Lin, Jhen-Yi Hong, Tsung-Wei Su, Bai-Jiun Kuo, Wei-Hsin Chang, Yi-Fan Tu & Yu-Chih Lo. (2017) Structural Insights into Linear Tri-ubiquitin Recognition by A20-Binding Inhibitor of NF-κB, ABIN-2. Structure 25:1, pages 66-78.
Crossref
Crossref
Ashish Shelar & Manju Bansal. (2016) Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:11, pages 2804-2817.
Crossref
Crossref
Balu Kamaraj & Rituraj Purohit. (2016) Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)-A Molecular Dynamics Approach. Journal of Cellular Biochemistry 117:11, pages 2608-2619.
Crossref
Crossref
Eleanor C. Law, Henry R. Wilman, Sebastian Kelm, Jiye Shi & Charlotte M. Deane. (2016) Examining the Conservation of Kinks in Alpha Helices. PLOS ONE 11:6, pages e0157553.
Crossref
Crossref
Shuguang Yuan, Slawomir Filipek & Horst Vogel. (2016) A Gating Mechanism of the Serotonin 5-HT 3 Receptor. Structure 24:5, pages 816-825.
Crossref
Crossref
Zhanyong Guo & Dieter Cremer. 2016. Reviews in Computational Chemistry. Reviews in Computational Chemistry
369
438
.
Renate Gessmann, Hans Brückner & Kyriacos Petratos. (2016)
The crystal structure of Z-(Aib)
10
-OH at 0.65 Å resolution: three complete turns of 3
10
-helix
. Journal of Peptide Science 22:2, pages 76-81.
Crossref
Crossref
Marc Perea, Ivar Lugtenburg, Eduardo Mayol, Arnau Cordomí, Xavier Deupí, Leonardo Pardo & Mireia Olivella. (2015) TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. BMC Bioinformatics 16:1.
Crossref
Crossref
Hyun Joo, Archana G. Chavan, Keith J. Fraga & Jerry Tsai. (2015) An amino acid code for irregular and mixed protein packing. Proteins: Structure, Function, and Bioinformatics 83:12, pages 2147-2161.
Crossref
Crossref
Prasun Kumar & Manju Bansal. (2015) Dissecting π-helices: sequence, structure and function. FEBS Journal 282:22, pages 4415-4432.
Crossref
Crossref
Jérémy Esque, Aurélie Urbain, Catherine Etchebest & Alexandre G. de Brevern. (2015) Sequence–structure relationship study in all-α transmembrane proteins using an unsupervised learning approach. Amino Acids 47:11, pages 2303-2322.
Crossref
Crossref
Prasun Kumar & Manju Bansal. (2015) Identification of local variations within secondary structures of proteins. Acta Crystallographica Section D Biological Crystallography 71:5, pages 1077-1086.
Crossref
Crossref
Shao-Qing Zhang, Daniel W. Kulp, Chaim A. Schramm, Marco Mravic, Ilan Samish & William F. DeGrado. (2015) The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions. Structure 23:3, pages 527-541.
Crossref
Crossref
Jiqing Guo, Yen May Cheng, James P. Lees-Miller, Laura L. Perissinotti, Tom W. Claydon, Christina M. Hull, Samrat Thouta, Daniel E. Roach, Serdar Durdagi, Sergei Y. Noskov & Henry J. Duff. (2015) NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation. Biophysical Journal 108:6, pages 1400-1413.
Crossref
Crossref
Christopher W. Wood, Marc Bruning, Amaurys Á. Ibarra, Gail J. Bartlett, Andrew R. Thomson, Richard B. Sessions, R Leo Brady & Derek N. Woolfson. (2014) CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics 30:21, pages 3029-3035.
Crossref
Crossref
Henry R. WilmanJean-Paul EbejerJiye Shi, Charlotte M. DeaneBernhard Knapp. (2014) Crowdsourcing Yields a New Standard for Kinks in Protein Helices. Journal of Chemical Information and Modeling 54:9, pages 2585-2593.
Crossref
Crossref
Henry R. Wilman, Jiye Shi & Charlotte M. Deane. (2014) Helix kinks are equally prevalent in soluble and membrane proteins. Proteins: Structure, Function, and Bioinformatics 82:9, pages 1960-1970.
Crossref
Crossref
Laura Dominguez, Leigh Foster, Stephen C. Meredith, John E. Straub & D. Thirumalai. (2014) Structural Heterogeneity in Transmembrane Amyloid Precursor Protein Homodimer Is a Consequence of Environmental Selection. Journal of the American Chemical Society 136:27, pages 9619-9626.
Crossref
Crossref
Xiuying Liu, Yan Yin, Jinjun Wu & Zhenfeng Liu. (2014) Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis. Nature Communications 5:1.
Crossref
Crossref
Xavier Deupi. (2014) Relevance of rhodopsin studies for GPCR activation. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837:5, pages 674-682.
Crossref
Crossref
Bhaskar Dasgupta, Sucharita Dey & Pinak Chakrabarti. (2014) Water and side-chain embedded π-turns. Biopolymers 101:5, pages 441-453.
Crossref
Crossref
Beom Sik Kang, Ku-Jin Kim & U Deok Seo. (2014) Reconstruction of α-helices in a Protein Molecule. KIPS Transactions on Software and Data Engineering 3:4, pages 163-168.
Crossref
Crossref
Bruno E. Correia, John T. Bates, Rebecca J. Loomis, Gretchen Baneyx, Chris Carrico, Joseph G. Jardine, Peter Rupert, Colin Correnti, Oleksandr Kalyuzhniy, Vinayak Vittal, Mary J. Connell, Eric Stevens, Alexandria Schroeter, Man Chen, Skye MacPherson, Andreia M. Serra, Yumiko Adachi, Margaret A. Holmes, Yuxing Li, Rachel E. Klevit, Barney S. Graham, Richard T. Wyatt, David Baker, Roland K. Strong, James E. Crowe, Philip R. Johnson & William R. Schief. (2014) Proof of principle for epitope-focused vaccine design. Nature 507:7491, pages 201-206.
Crossref
Crossref
Mireia Olivella, Gianluigi Caltabiano & Arnau Cordomí. (2013) The role of Cysteine 6.47 in class A GPCRs. BMC Structural Biology 13:1.
Crossref
Crossref
Zhanyong Guo, Elfi Kraka & Dieter Cremer. (2013) Description of local and global shape properties of protein helices. Journal of Molecular Modeling 19:7, pages 2901-2911.
Crossref
Crossref
Sumire Nakamura, Takeshi Itabashi, Daisuke Ogawa & Tetsuji Okada. (2013) Common and distinct mechanisms of activation of rhodopsin and other G protein-coupled receptors. Scientific Reports 3:1.
Crossref
Crossref
R. Wu, M. Gu, R. Wilton, G. Babnigg, Y. Kim, P. R. Pokkuluri, H. Szurmant, A. Joachimiak & M. Schiffer. (2013)
Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of
Bacillus subtilis
histidine kinase, KinD
. Protein Science 22:5, pages 564-576.
Crossref
Crossref
Chen Wang, Jiayan Sang, Jiawei Wang, Mingyan Su, Jennifer S. Downey, Qinggan Wu, Shida Wang, Yongfei Cai, Xiaozheng Xu, Jun Wu, Dilani B. Senadheera, Dennis G. Cvitkovitch, Lin Chen, Steven D. Goodman & Aidong Han. (2013) Mechanistic Insights Revealed by the Crystal Structure of a Histidine Kinase with Signal Transducer and Sensor Domains. PLoS Biology 11:2, pages e1001493.
Crossref
Crossref
Sandip V. Jadhav, Anupam Bandyopadhyay & Hosahudya N. Gopi. (2013)
Protein secondary structure mimetics: crystal conformations of α/γ
4
-hybrid peptide12-helices with proteinogenic side chains and their analogy with α- and β-peptide helices
. Org. Biomol. Chem. 11:3, pages 509-514.
Crossref
Crossref
R. S. K. Vijayan, Neha Trivedi, Sudipendra Nath Roy, Indrani Bera, Prabu Manoharan, Pavan V. Payghan, Dhananjay Bhattacharyya & Nanda Ghoshal. (2012)
Modeling the Closed and Open State Conformations of the GABA
A
Ion Channel - Plausible Structural Insights for Channel Gating
. Journal of Chemical Information and Modeling 52:11, pages 2958-2969.
Crossref
Crossref
Renate Gessmann, Danny Axford, Gwyndaf Evans, Hans Brückner & Kyriacos Petratos. (2012) The crystal structure of samarosporin I at atomic resolution. Journal of Peptide Science 18:11, pages 678-684.
Crossref
Crossref
Ayelet Benjamini & Berend Smit. (2012) Robust Driving Forces for Transmembrane Helix Packing. Biophysical Journal 103:6, pages 1227-1235.
Crossref
Crossref
Anna Caroline E. Dahl, Matthieu Chavent & Mark S. P. Sansom. (2012) Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 28:16, pages 2193-2194.
Crossref
Crossref
Gursharan K. Bains, Sea H. Kim, Eric J. Sorin & Vasanthy Narayanaswami. (2012) The Extent of Pyrene Excimer Fluorescence Emission Is a Reflector of Distance and Flexibility: Analysis of the Segment Linking the LDL Receptor-Binding and Tetramerization Domains of Apolipoprotein E3. Biochemistry 51:31, pages 6207-6219.
Crossref
Crossref
Atya Aziz, John F. Hess, Madhu S. Budamagunta, John C. Voss, Alexandre P. Kuzin, Yuanpeng J. Huang, Rong Xiao, Gaetano T. Montelione, Paul G. FitzGerald & John F. Hunt. (2012) The Structure of Vimentin Linker 1 and Rod 1B Domains Characterized by Site-directed Spin-labeling Electron Paramagnetic Resonance (SDSL-EPR) and X-ray Crystallography. Journal of Biological Chemistry 287:34, pages 28349-28361.
Crossref
Crossref
Angel Gonzalez, Arnau Cordomí, Gianluigi Caltabiano & Leonardo Pardo. (2012) Impact of Helix Irregularities on Sequence Alignment and Homology Modeling of G Protein‐Coupled Receptors. ChemBioChem 13:10, pages 1393-1399.
Crossref
Crossref
Hyun Joo, Archana G. Chavan, Jamie Phan, Ryan Day & Jerry Tsai. (2012) An Amino Acid Packing Code for α-Helical Structure and Protein Design. Journal of Molecular Biology 419:3-4, pages 234-254.
Crossref
Crossref
Chaim A. Schramm, Brett T. Hannigan, Jason E. Donald, Chen Keasar, Jeffrey G. Saven, William F. DeGrado & Ilan Samish. (2012) Knowledge-Based Potential for Positioning Membrane-Associated Structures and Assessing Residue-Specific Energetic Contributions. Structure 20:5, pages 924-935.
Crossref
Crossref
Brian J. Smith. (2012) PS – a program for the analysis of helix geometry. Journal of Molecular Graphics and Modelling 33, pages 52-60.
Crossref
Crossref
Renate Gessmann, Danny Axford, Robin L. Owen, Hans Brückner & Kyriacos Petratos. (2012)
Four complete turns of a curved 3
10
-helix at atomic resolution: the crystal structure of the peptaibol trichovirin I-4A in a polar environment suggests a transition to α-helix for membrane function
. Acta Crystallographica Section D Biological Crystallography 68:2, pages 109-116.
Crossref
Crossref
Xavier Deupi. 2012. Membrane Protein Structure and Dynamics. Membrane Protein Structure and Dynamics
219
235
.
Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann & Andreas Hildebrandt. (2011) String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins. Journal of Chemical Information and Modeling 51:11, pages 3017-3025.
Crossref
Crossref
Yohann Mansiaux, Agnel Praveen Joseph, Jean-Christophe Gelly & Alexandre G. de Brevern. (2011) Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship. PLoS ONE 6:3, pages e18401.
Crossref
Crossref
K. Sansuk, X. Deupi, I. R. Torrecillas, A. Jongejan, S. Nijmeijer, R. A. Bakker, L. Pardo & R. Leurs. (2010) A Structural Insight into the Reorientation of Transmembrane Domains 3 and 5 during Family A G Protein-Coupled Receptor Activation. Molecular Pharmacology 79:2, pages 262-269.
Crossref
Crossref
Sunil Kumar Tewary, Toshiro Oda, Amy Kendall, Wen Bian, Gerald Stubbs, Sek-Man Wong & Kunchithapadam Swaminathan. (2011) Structure of Hibiscus Latent Singapore Virus by Fiber Diffraction: A Nonconserved His122 Contributes to Coat Protein Stability. Journal of Molecular Biology 406:3, pages 516-526.
Crossref
Crossref
Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung & Wen-Lian Hsu. (2011) TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. Nucleic Acids Research 39:suppl_1, pages D347-D355.
Crossref
Crossref
Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita & Kenji Mizuguchi. (2010) Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. BMC Bioinformatics 11:1.
Crossref
Crossref
Agnel Praveen Joseph, Aurélie Bornot & Alexandre G. de Brevern. 2010. Introduction to Protein Structure Prediction. Introduction to Protein Structure Prediction
75
105
.
Jean Pylouster, Aurélie Bornot, Catherine Etchebest & Alexandre G. de Brevern. (2010) Influence of assignment on the prediction of transmembrane helices in protein structures. Amino Acids 39:5, pages 1241-1254.
Crossref
Crossref
Catherine Etchebest & Gaelle Debret. 2010. Membrane Protein Structure Determination. Membrane Protein Structure Determination
363
385
.
Douglas G. Metcalf, Dan W. Kulp, Joel S. Bennett & William F. DeGrado. (2009) Multiple Approaches Converge on the Structure of the Integrin αIIb/β3 Transmembrane Heterodimer. Journal of Molecular Biology 392:4, pages 1087-1101.
Crossref
Crossref
Manoj Tyagi, Aurélie Bornot, Bernard Offmann & Alexandre G. de Brevern. (2009) Analysis of loop boundaries using different local structure assignment methods. Protein Science 18:9, pages 1869-1881.
Crossref
Crossref
Sushilee Ranganathan, Dmitry Izotov, Elfi Kraka & Dieter Cremer. (2009) Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method. Proteins: Structure, Function, and Bioinformatics 76:2, pages 418-438.
Crossref
Crossref
Abiola M. Pollard, Alexandrine M. Bilwes & Brian R. Crane. (2009) The Structure of a Soluble Chemoreceptor Suggests a Mechanism for Propagating Conformational Signals. Biochemistry 48:9, pages 1936-1944.
Crossref
Crossref
R. Sreekanth, Vasantha Pattabhi & S.S. Rajan. (2008) Characterization of alpha helices interacting with nucleic acids. Computational Biology and Chemistry 32:5, pages 378-381.
Crossref
Crossref
Suren A. Tatulian. (2008) Determination of helix orientations in proteins. Computational Biology and Chemistry 32:5, pages 370-374.
Crossref
Crossref
Purevjav Enkhbayar, Sodov Damdinsuren, Mitsuru Osaki & Norio Matsushima. (2008) HELFIT: Helix fitting by a total least squares method. Computational Biology and Chemistry 32:4, pages 307-310.
Crossref
Crossref
ALAIN GORIELY, ANDREW HAUSRATH & SÉBASTIEN NEUKIRCH. (2011) THE DIFFERENTIAL GEOMETRY OF PROTEINS AND ITS APPLICATIONS TO STRUCTURE DETERMINATION. Biophysical Reviews and Letters 03:01n02, pages 77-101.
Crossref
Crossref
R. Peter Riek, Angela A. Finch, Gillian E. Begg & Robert M. Graham. (2008) Wide Turn Diversity in Protein Transmembrane Helices Implications for G-Protein-Coupled Receptor and Other Polytopic Membrane Protein Structure and Function. Molecular Pharmacology 73:4, pages 1092-1104.
Crossref
Crossref
Jennifer R. Calhoun, Weixia Liu, Katrin Spiegel, Matteo Dal Peraro, Michael L. Klein, Kathleen G. Valentine, A. Joshua Wand & William F. DeGrado. (2008) Solution NMR Structure of a Designed Metalloprotein and Complementary Molecular Dynamics Refinement. Structure 16:2, pages 210-215.
Crossref
Crossref
Hui Sun Lee, Jiwon Choi & Sukjoon Yoon. (2007) QHELIX: A Computational Tool for the Improved Measurement of Inter-Helical Angles in Proteins. The Protein Journal 26:8, pages 556-561.
Crossref
Crossref
Anne Marie Jørgensen, Lena Tagmose, Anne Marie M. Jørgensen, Klaus P. Bøgesø & Günther H. Peters. (2007) Molecular Dynamics Simulations of Na+/Cl−-Dependent Neurotransmitter Transporters in a Membrane-Aqueous System. ChemMedChem 2:6, pages 827-840.
Crossref
Crossref
Anne Marie Jørgensen, Lena Tagmose, Anne Marie M. Jørgensen, Sid Topiol, Michael Sabio, Klaus Gundertofte, Klaus P. Bøgesø & Günther H. Peters. (2007) Homology Modeling of the Serotonin Transporter: Insights into the Primary Escitalopram-binding Site. ChemMedChem 2:6, pages 815-826.
Crossref
Crossref
Jinhyuk Lee & Wonpil Im. (2007) Implementation and application of helix–helix distance and crossing angle restraint potentials. Journal of Computational Chemistry 28:3, pages 669-680.
Crossref
Crossref
Leonardo Pardo, Xavier Deupi, Nicole Dölker, María Luz López-Rodríguez & Mercedes Campillo. (2007) The Role of Internal Water Molecules in the Structure and Function of the Rhodopsin Family of G Protein-Coupled Receptors. ChemBioChem 8:1, pages 19-24.
Crossref
Crossref
R. Sreekanth & S.S. Rajan. (2007) The study of helical distortions due to environmental changes: Choice of parameters. Biophysical Chemistry 125:1, pages 191-200.
Crossref
Crossref
Lipi Thukral, Sandhya R Shenoy, Kumkum Bhushan & B Jayaram. (2007) ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins. Journal of Biosciences 32:1, pages 71-81.
Crossref
Crossref
Michael Petukhov, Dmitry Lebedev, Valery Shalguev, Akhmed Islamov, Aleksandr Kuklin, Vladislav Lanzov & Vladimir Isaev-Ivanov. (2006) Conformational flexibility of RecA protein filament: Transitions between compressed and stretched states. Proteins: Structure, Function, and Bioinformatics 65:2, pages 296-304.
Crossref
Crossref
Katrin Spiegel, William F. De Grado & Michael L. Klein. (2006) Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations. Proteins: Structure, Function, and Bioinformatics 65:2, pages 317-330.
Crossref
Crossref
Jenny Mackenzie, Lise Pedersen, Susan Arent & Anette Henriksen. (2006) Controlling Electron Transfer in Acyl-CoA Oxidases and Dehydrogenases. Journal of Biological Chemistry 281:41, pages 31012-31020.
Crossref
Crossref
R. F. S. Walters & W. F. DeGrado. (2006) Helix-packing motifs in membrane proteins. Proceedings of the National Academy of Sciences 103:37, pages 13658-13663.
Crossref
Crossref
Nicholas M. GlykosYannis PapanikolauMetaxia VlassiDina KotsifakiGiovanni CesareniMichael Kokkinidis. (2006) Loopless Rop: Structure and Dynamics of an Engineered Homotetrameric Variant of the Repressor of Primer Protein. Biochemistry 45:36, pages 10905-10919.
Crossref
Crossref
Purevjav Enkhbayar, Kunio Hikichi, Mitsuru Osaki, Robert H. Kretsinger & Norio Matsushima. (2006) 310-helices in proteins are parahelices. Proteins: Structure, Function, and Bioinformatics 64:3, pages 691-699.
Crossref
Crossref
Zhiyi Wei, Yanyan Xue, Hang Xu & Weimin Gong. (2006) Crystal Structure of the C-terminal Domain of S.cerevisiae eIF5. Journal of Molecular Biology 359:1, pages 1-9.
Crossref
Crossref
Mihaly Mezei & Marta Filizola. (2006) TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. Journal of Computer-Aided Molecular Design 20:2, pages 97-107.
Crossref
Crossref
Vikas Nanda & William F. DeGrado. (2005) Computational Design of Heterochiral Peptides against a Helical Target. Journal of the American Chemical Society 128:3, pages 809-816.
Crossref
Crossref
Juliette Martin, Guillaume Letellier, Antoine Marin, Jean-François Taly, Alexandre G de Brevern & Jean-François Gibrat. (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Structural Biology 5:1.
Crossref
Crossref
Indraneel Majumdar, S Sri Krishna & Nick V Grishin. (2005) PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 6:1.
Crossref
Crossref
Silvano Geremia, Luigi Di Costanzo, Lucio Randaccio, Donald E. Engel, Angela Lombardi, Flavia Nastri & William F. DeGrado. (2005) Response of a Designed Metalloprotein to Changes in Metal Ion Coordination, Exogenous Ligands, and Active Site Volume Determined by X-ray Crystallography. Journal of the American Chemical Society 127:49, pages 17266-17276.
Crossref
Crossref
Donald E. Engel & William F. DeGrado. (2005) α-α linking motifs and interhelical orientations. Proteins: Structure, Function, and Bioinformatics 61:2, pages 325-337.
Crossref
Crossref
Catherine Etchebest, Cristina Benros, Serge Hazout & Alexandre G. de Brevern. (2005) A structural alphabet for local protein structures: Improved prediction methods. Proteins: Structure, Function, and Bioinformatics 59:4, pages 810-827.
Crossref
Crossref
Arnab Bhattacharjee & Manju Bansal. (2005) Collagen Structure: The Madras Triple Helix and the Current Scenario. IUBMB Life (International Union of Biochemistry and Molecular Biology: Life) 57:3, pages 161-172.
Crossref
Crossref
Tobias S. Ulmer, Ad Bax, Nelson B. Cole & Robert L. Nussbaum. (2005) Structure and Dynamics of Micelle-bound Human α-Synuclein. Journal of Biological Chemistry 280:10, pages 9595-9603.
Crossref
Crossref
Steven J. Lahr, Donald E. Engel, Steven E. Stayrook, Ornella Maglio, Benjamin North, Silvano Geremia, Angela Lombardi & William F. DeGrado. (2005) Analysis and Design of Turns in α-Helical Hairpins. Journal of Molecular Biology 346:5, pages 1441-1454.
Crossref
Crossref
Marina Gimpelev, Lucy R. Forrest, Diana Murray & Barry Honig. (2004) Helical Packing Patterns in Membrane and Soluble Proteins. Biophysical Journal 87:6, pages 4075-4086.
Crossref
Crossref
Pranab K. Mohapatra, Adikanda Khamari & Mukesh K. Raval. (2004) A method for structural analysis of α-helices of membrane proteins. Journal of Molecular Modeling 10:5-6, pages 393-398.
Crossref
Crossref
Hay Dvir, Michal Harel, Suzanne Bon, Wang-Qing Liu, Michel Vidal, Christiane Garbay, Joel L Sussman, Jean Massoulié & Israel Silman. (2004) The synaptic acetylcholinesterase tetramer assembles around a polyproline II helix. The EMBO Journal 23:22, pages 4394-4405.
Crossref
Crossref
Lin Liu, Zhiyi Wei, Yanli Wang, Mao Wan, Zhongjun Cheng & Weimin Gong. (2004) Crystal Structure of Human Coactosin-like Protein. Journal of Molecular Biology 344:2, pages 317-323.
Crossref
Crossref
Ingo P Korndörfer, Monica K Dommel & Arne Skerra. (2004) Structure of the periplasmic chaperone Skp suggests functional similarity with cytosolic chaperones despite differing architecture. Nature Structural & Molecular Biology 11:10, pages 1015-1020.
Crossref
Crossref
Xavier Deupi, Mireia Olivella, Cedric Govaerts, Juan Antonio Ballesteros, Mercedes Campillo & Leonardo Pardo. (2004) Ser and Thr Residues Modulate the Conformation of Pro-Kinked Transmembrane α-Helices. Biophysical Journal 86:1, pages 105-115.
Crossref
Crossref
Renate Gessmann, Hans Brückner & Kyriacos Petratos. (2003)
Three complete turns of a 3
10
-helix at atomic resolution: the crystal structure of Z-(Aib)
11
-O
t
Bu
. Journal of Peptide Science 9:11-12, pages 753-762.
Crossref
Crossref
Bernhard Loll, Grzegorz Raszewski, Wolfram Saenger & Jacek Biesiadka. (2003) Functional Role of Cα–H⋯O Hydrogen Bonds Between Transmembrane α-Helices in Photosystem I. Journal of Molecular Biology 328:3, pages 737-747.
Crossref
Crossref
Joanne N. BrightMark S. P. Sansom. (2002) The Flexing/Twirling Helix: Exploring the Flexibility about Molecular Hinges Formed by Proline and Glycine Motifs in Transmembrane Helices. The Journal of Physical Chemistry B 107:2, pages 627-636.
Crossref
Crossref
Frank S. Cordes, Joanne N. Bright & Mark S.P. Sansom. (2002) Proline-induced Distortions of Transmembrane Helices. Journal of Molecular Biology 323:5, pages 951-960.
Crossref
Crossref
Joanne N. Bright, Indira H. Shrivastava, Frank S. Cordes & Mark S. P. Sansom. (2002) Conformational dynamics of helix S6 from Shaker potassium channel: Simulation studies. Biopolymers 64:6, pages 303-313.
Crossref
Crossref
M.N. Fodje & S. Al-Karadaghi. (2002) Occurrence, conformational features and amino acid propensities for the π-helix. Protein Engineering, Design and Selection 15:5, pages 353-358.
Crossref
Crossref
Alessandro Senes, Iban Ubarretxena-Belandia & Donald M. Engelman. (2001) The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. Proceedings of the National Academy of Sciences 98:16, pages 9056-9061.
Crossref
Crossref
Sandeep Kumar & Ruth Nussinov. (2000) Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper. Proteins: Structure, Function, and Genetics 41:4, pages 485-497.
Crossref
Crossref