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Memoir: template-based structure prediction for membrane proteins

Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2013 Nucleic Acids Research  
As a result, for a membrane protein of interest, the much-needed structural information usually comes from a homology model.  ...  Current homology modelling software is optimized for globular proteins, and ignores the constraints that the membrane is known to place on protein structure.  ...  ACKNOWLEDGEMENTS We would like to thank our fellow members of the Oxford Protein Informatics Group for useful discussions.  ... 
doi:10.1093/nar/gkt331 pmid:23640332 pmcid:PMC3692111 fatcat:az47ghyxfrfjbo4s2qz4inizji

Francis Harry Compton Crick OM. 8 June 1916 — 28 July 2004

Mark S. Bretscher, Graeme Mitchison
2017 Biographical Memoirs of Fellows of the Royal Society  
We also thank Annette Faux, Michael Fuller, Richard Henderson, Christof Koch, Peter Lawrence and Robert Olby for advice about different aspects of the Memoir, and Annette Faux for help with the figures  ...  We thank them for permission to reproduce some of their family photographs.  ...  In the latter case, they suggested that an extra base in the template would, during protein synthesis, change the reading phase in the template so that a nonsensical polypeptide was produced after that  ... 
doi:10.1098/rsbm.2017.0010 fatcat:hg6hc5svlfd67czgsyvqozadoy

Jean Brachet, 19 March 1909 - 10 August 1988

Norman Wingate Pirie
1990 Biographical Memoirs of Fellows of the Royal Society  
He said that he failed repeatedly in biology examinations because of his dislike for classification.  ...  Experience in hospitals and clinics convinced him that he was temperamentally unsuited for medicine.  ...  Finally, each specific RNA molecule would act as a template for a specific protein'. That foreshadowed the concept of messenger RNA (mRNA).  ... 
doi:10.1098/rsbm.1990.0025 fatcat:bfilcv3wrrestmlshf2nvhi63u

Clement Henry Bamford. 10 October 1912 - 7 November 1999: Elected F.R.S. 1964

W. J. Feast
2004 Biographical Memoirs of Fellows of the Royal Society  
associated with any of his research areas would be well advised to consult this archive, which contains more insight and interest than it was possible to contain within the confines of this biographical memoir  ...  This analysis of a lot of accumulated data on copolymerizations led to a reliable scheme for predicting reactivity ratios and chain transfer coefficients. A. D.  ...  Readers of these memoirs will know that the dilemma of a choice between a career in science or music is more common than Bam's inquisitors imagined.  ... 
doi:10.1098/rsbm.2004.0001 fatcat:jly4im5xrndfbnppqlcl7qaddq

Computational modeling of membrane proteins

Julia Koehler Leman, Martin B. Ulmschneider, Jeffrey J. Gray
2014 Proteins: Structure, Function, and Bioinformatics  
The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions.  ...  The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure  ...  We are also very grateful for the valuable comments from Kalina Hristova and Oliver Beckstein after proofreading the manuscript.  ... 
doi:10.1002/prot.24703 pmid:25355688 pmcid:PMC4270820 fatcat:lk7ku2koqnfi5axp7luxq6e44e

Membrane proteins structures: A review on computational modeling tools

Jose G. Almeida, Antonio J. Preto, Panagiotis I. Koukos, Alexandre M.J.J. Bonvin, Irina S. Moreira
2017 Biochimica et Biophysica Acta - Biomembranes  
It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML).  ...  Current approaches are usually based on a combination of homology modeling 10 or de novo protein structure determination 11 with ML algorithms 12 to predict binding interfaces and/or intermolecular contacts  ...  Some methods have been developed specifically for membrane protein modelling, namely MEMOIR (Membrane protein modelling pipeline), 67 which can model the 3D structure of a protein of known sequence  ... 
doi:10.1016/j.bbamem.2017.07.008 pmid:28716627 fatcat:sgfs7jbdqbeqnbommmfej4vvqe

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy

Vachiranee Limviphuvadh, Chee Seng Tan, Fumikazu Konishi, Piroon Jenjaroenpun, Joy Shengnan Xiang, Yuliya Kremenska, Yar Soe Mu, Nicholas Syn, Soo Chin Lee, Ross A. Soo, Frank Eisenhaber, Sebastian Maurer-Stroh (+1 others)
2018 BMC Cancer  
After that, we used five computational criteria to prioritize the SNPs based on their importance for protein function.  ...  The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy  ...  Therefore, we used another software called Memoir [40] which is a homology modelling algorithm designed specifically for membrane proteins.  ... 
doi:10.1186/s12885-018-4471-x pmid:29751792 pmcid:PMC5948914 fatcat:5265if2wvfgmpoks7hch6akkwu

AlignMe—a membrane protein sequence alignment web server

Marcus Stamm, René Staritzbichler, Kamil Khafizov, Lucy R. Forrest
2014 Nucleic Acids Research  
We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe.  ...  These settings utilize different types of inputs: (positionspecific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity  ...  , Garching, Germany for servers and assistance.  ... 
doi:10.1093/nar/gku291 pmid:24753425 pmcid:PMC4086118 fatcat:mwdgbn7phvbgbhx4w6x2toxpfi

Automated Procedure for Contact-Map-Based Protein Structure Reconstruction

Bogumil M. Konopka, Marika Ciombor, Monika Kurczynska, Malgorzata Kotulska
2014 Journal of Membrane Biology  
Therefore, a number of procedures for protein structure prediction based on their contact-map have been proposed. Their comparison is difficult due to different methodologies used for validation.  ...  In this work, a Contact Map-to-Structure pipeline (C2S_pipeline) for contact-based protein structure reconstruction is designed and validated.  ...  Part of the calculations was performed in Wrocław Centre for Networking and Supercomputing.  ... 
doi:10.1007/s00232-014-9648-x pmid:24682239 pmcid:PMC3983884 fatcat:jmlfbo3s7nebdgooldi32su2ka

Identification of lipid A deacylase as a novel, highly conserved and protective antigen against enterohemorrhagic Escherichia coli

Maricarmen Rojas-Lopez, Manuele Martinelli, Valentina Brandi, Grégory Jubelin, Fabio Polticelli, Marco Soriani, Mariagrazia Pizza, Mickaël Desvaux, Roberto Rosini
2019 Scientific Reports  
Twenty-four potential protein antigens were identified and one of them (MC001) was successfully expressed onto Generalized Modules for Membrane Antigens (GMMA) delivery system.  ...  While vaccine development is warranted, a licensed vaccine, specific for human use, against EHEC is not yet available.  ...  Wood and Chen, Poyin for English language editing.  ... 
doi:10.1038/s41598-019-53197-z pmid:31745113 pmcid:PMC6863877 fatcat:jwgnlbc52jel3cp6tsvefyarru

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf, Garegin A. Papoian
2018 PLoS Computational Biology  
Zinc is an essential trace element with 10% of the proteins in the human proteome capable of zinc binding. Thus, zinc deficiency or impairment of zinc homeostasis disrupt key cellular functions.  ...  These computational findings were functionally validated using site-directed mutagenesis of ZnT2 residues predicted to reside along the putative zinc permeation pathway and zinc transport assay.  ...  Modeling of ZnT2 was carried out by Memoir method [25] , specifically designed to exploit the structural constraints imposed by membrane proteins.  ... 
doi:10.1371/journal.pcbi.1006503 fatcat:6efovamy2bdrrl7brv2r77fwve

Integrative modeling of membrane-associated protein assemblies

Jorge Roel-Touris, Brian Jiménez-García, Alexandre M. J. J. Bonvin
2020 Nature Communications  
Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies.  ...  The increased number of deposited structures of membrane proteins has opened the route to modeling their complexes by methods such as docking.  ...  Acknowledgements We would like to thank all the Computational Structural Biology group at Utrecht University and specially Dr. Panagiotis Koukos for all the useful insights and fruitful discussions.  ... 
doi:10.1038/s41467-020-20076-5 pmid:33277503 fatcat:bmfjrilgevbhdp4jzhk42juxha

Integrative Modeling of Membrane-associated Protein Assemblies [article]

Jorge L Roel-Touris, Brian Jiménez-García, Alexandre MJJ Bonvin
2020 bioRxiv   pre-print
Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies, specifically complexes consisting of a membrane-embedded protein and a soluble partner  ...  Historically, membrane protein systems have been considered as one of the most challenging systems to study with experimental structural biology techniques.  ...  Such membrane-specific scoring functions have been already shown appropriate for membrane protein structure prediction and design purposes 45 and might also represent a significant advance for membrane-associated  ... 
doi:10.1101/2020.07.20.211987 fatcat:sdtrkyyarvdf3imvd2oh4lofzy

Network topology of NaV1.7 mutations in sodium channel-related painful disorders

Dimos Kapetis, Jenny Sassone, Yang Yang, Barbara Galbardi, Markos N. Xenakis, Ronald L. Westra, Radek Szklarczyk, Patrick Lindsey, Catharina G. Faber, Monique Gerrits, Ingemar S. J. Merkies, Sulayman D. Dib-Hajj (+3 others)
2017 BMC Systems Biology  
There is a need for better understanding of how gain-of-function mutations alter the atomic structure of Nav1.7.  ...  Results: We used homology modeling to build an atomic model of NaV1.7 and a network-based theoretical approach, which can predict interatomic interactions and connectivity arrangements, to investigate  ...  We constructed the atomic model of NaV1.7 sodium channel using the MEMOIR server [38] based on the crystal structure of the bacterial Arcobacter bultzeri NaV channel NaVAb as a template with the human  ... 
doi:10.1186/s12918-016-0382-0 pmid:28235406 pmcid:PMC5324268 fatcat:ivsi3ukjojeb3auzxnbuevc6ze

Molecules into Cells: Specifying Spatial Architecture

F. M. Harold
2005 Microbiology and Molecular Biology Reviews  
These membrane proteins, and biosynthetic proteins too, must be targeted to their cognate membranes, recognizing ligand proteins or specific lipids.  ...  an external template or global plan.  ... 
doi:10.1128/mmbr.69.4.544-564.2005 pmid:16339735 pmcid:PMC1306800 fatcat:c2uommtkbndujd4nwr2otj3hnu
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