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Modeling protein structure at near atomic resolutions with Gorgon

Matthew L. Baker, Sasakthi S. Abeysinghe, Stephen Schuh, Ross A. Coleman, Austin Abrams, Michael P. Marsh, Corey F. Hryc, Troy Ruths, Wah Chiu, Tao Ju
2011 Journal of Structural Biology  
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions.  ...  Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models.  ...  Additionally we would like to thank Brian Chen and Paul Heider for their contributions to the Gorgon source code.  ... 
doi:10.1016/j.jsb.2011.01.015 pmid:21296162 pmcid:PMC3078171 fatcat:sznwv5jhtnef5dac7l5zw2dxay

A method for simultaneous alignment of multiple protein structures

Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
2004 Proteins: Structure, Function, and Bioinformatics  
MultiProt finds the common geometrical cores between input molecules. To date, most methods for multiple alignment start from the pairwise alignment solutions.  ...  These include: (1) a partial alignment of hinge-bent domains; (2) identification of functional groups of G-proteins; (3) analysis of binding sites; and (4) protein-protein interface alignment.  ...  This research has been supported in part by the "Center of Excellence in Geometric Computing and its Applications" funded by the Israel Science Foundation (administered by the Israel Academy of Sciences  ... 
doi:10.1002/prot.10628 pmid:15162494 fatcat:4nbsroksbbhp7p3hr2krvdycrq

Foldons, protein structural modules, and exons

A. R. Panchenko, Z. Luthey-Schulten, P. G. Wolynes
1996 Proceedings of the National Academy of Sciences of the United States of America  
The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied.  ...  Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of  ...  We thank Kris Koretke for her generous help in the initial stages of the project and Jeff Saven and John Portman for helpful discussions. We thank J. N. Onuchic, K. Schulten, and S.  ... 
doi:10.1073/pnas.93.5.2008 pmid:8700876 pmcid:PMC39900 fatcat:segtmcmcb5dmvpsdzqbtmqlakm

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture

Jose Hleap, Edward Susko, Christian Blouin
2013 BMC Structural Biology  
We propose a graph-theory approach with significance and power testing to identify modules in protein structures.  ...  Our inferred dynamic modules in the protein NPC1 are also shown to match functional components of the protein related to the NPC1 disease.  ...  To Wilson Chan for some of the molecular dynamic simulations, Alex Safatli and Kyle Nguyen for the collaboration in some of the code.  ... 
doi:10.1186/1472-6807-13-20 pmid:24131821 pmcid:PMC4016585 fatcat:kflxfsb7xfeunjvwm5arm7ido4

Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems [chapter]

Didier Barradas-Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández-Recio
2018 Advances in Protein Chemistry and Structural Biology  
the interacting molecules, and ii) scoring for the identification of the correct orientations.  ...  Indeed, structural characterization of protein-protein interactions at atomic resolution has many applications in biomedicine, from diagnosis and vaccine design, to drug discovery.  ...  Two major technical aspects can be found in the majority of docking methods: the generation of a large variety of structural models (sampling) and the identification of the correct docking poses with a  ... 
doi:10.1016/bs.apcsb.2017.06.003 pmid:29412997 fatcat:6dsojxsybrfrthdz3yhlqmplxu

Computational methods for the prediction of protein folds

Thomas Dandekar, Rainer König
1997 Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology  
Frank Eisenhaber and Dr. Burkhard Rost for stimulating discussions, Dr. Thomas Creighton and Dr. Toby Gibson for critical reading of the manuscript, and Dr. Michelle Stewart as well aś Dr.  ...  Mark Nichols for stylistic corrections.  ...  For 16 of 30 proteins studied, they correlated with geometrically defined structural modules, but only weakly with exons.  ... 
doi:10.1016/s0167-4838(97)00132-5 pmid:9428653 fatcat:dmoosr6pfzfmljdtvzldfml62u

Protein structure prediction by AlphaFold2: are attention and symmetries all you need?

Nazim Bouatta, Peter Sorger, Mohammed AlQuraishi
2021 Acta Crystallographica Section D: Structural Biology  
reasoning over protein structures in three dimensions and (iii) end-to-end differentiability as a unifying framework for learning from protein data.  ...  The functions of most proteins result from their 3D structures, but determining their structures experimentally remains a challenge, despite steady advances in crystallography, NMR and single-particle  ...  PKS is a member of the SAB or Board of Directors of Merrimack Pharmaceutical, Glencoe Software, Applied Biomath, RareCyte and Nano-String, and has equity in several of these companies.  ... 
doi:10.1107/s2059798321007531 pmid:34342271 pmcid:PMC8329862 fatcat:sam47cns4fhg3hgo273qoshlta

From Structure to Function: Methods and Applications

Haim Wolfson, Maxim Shatsky, Dina Schneidman-Duhovny, Oranit Dror, Alexandra Shulman-Peleg, Buyong Ma, Ruth Nussinov
2005 Current protein and peptide science  
The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations.  ...  The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein  ...  ACKNOWLEDGEMENTS We thank our Structural Bioinformatics Group in Tel Aviv and in Frederick. The research of R. Nussinov and H. J.  ... 
doi:10.2174/1389203053545435 pmid:15853653 fatcat:t6se7n6msnhsfe54rss2xrvnhe

Structure calculation strategies for helical membrane proteins; a comparison study [article]

Ileana Stoica
2005 arXiv   pre-print
Structure predictions of helical membrane proteins have been designed to take advantage of the structural autonomy of secondary structure elements, as postulated by the two-stage model of Engelman and  ...  In this context, we investigate structure calculation strategies for two membrane proteins with different functions, sizes, aminoacid compositions, and topologies: the glycophorin A homodimer (a paradigm  ...  Acknowledgments This work was started at the Univ. of Ottawa. The author wishes to gratefully acknowledge Dr. Natalie Goto for valuable discussions and for an NMR spectroscopist's perspective.  ... 
arXiv:q-bio/0505014v4 fatcat:ir3btwyeffg7xdn252iwd2uei4

Solution structure of a type 2 module from fibronectin: implications for the structure and function of the gelatin-binding domain

Andrew R Pickford, Jennifer R Potts, Jeremy R Bright, Isabelle Phan, Iain D Campbell
1997 Structure  
The tertiary structure of the 1 F2 module is similar to that of a shorter F2 module, PDC-109b, from the bovine seminal plasma protein PDC-109.  ...  Knowledge of the structure of fibronectin will provide insights into its interactions with other proteins, and will contribute to our understanding of the structure and function of the extracellular matrix  ...  Acknowledgements The authors would like to thank Tony Willis, Robin Aplin and David Doak for their help and advice in matters of N-terminal sequence analysis, electrospray mass spectrometry and computation  ... 
doi:10.1016/s0969-2126(97)00193-7 pmid:9083105 fatcat:cyajmgoxljfdfivstrpclrrr5q

Using Xplor–NIH for NMR molecular structure determination

2006 Progress in nuclear magnetic resonance spectroscopy  
In particular, the Xplor-NIH software package owes a great debt to Axel Brünger as the original creator of XPLOR.  ...  In addition, major contributions have been made by Michael Nilges and the original developers of CHARMM [80] and CNS [16] .  ...  These include parameter and topology sets for proteins and nucleic acids adapted for purely geometric refinements, which we recommend for NMR refinement.  ... 
doi:10.1016/j.pnmrs.2005.10.001 fatcat:qmrva7pvv5fi7dw3e4qp2g5baq

A Structure-Controlled Investigation of Lipase Enantioselectivity by a Path-Planning Approach

David Guieysse, Juan Cortés, Sophie Puech-Guenot, Sophie Barbe, Vincent Lafaquière, Pierre Monsan, Thierry Siméon, Isabelle André, Magali Remaud-Siméon
2008 ChemBioChem  
Acknowledgements This work was supported by the Institut des Technologies Avan-cØes du Vivant (ITAV), Toulouse Canceropole campus.  ...  These structures, in which the given substrate is in a catalytic position but not bound to the enzyme, were subsequently minimized in order to correct the hybridization of the carbonyl function from sp  ...  proteins [20] and DNA, [21] or conformational changes due to protein loop motions [22] and protein domain motions  ... 
doi:10.1002/cbic.200700548 pmid:18418817 fatcat:o2gkafk6r5cjfo4n4p2crzgya4

Triage protein fold prediction

Hongxian He, Gregory McAllister, Temple F. Smith
2002 Proteins: Structure, Function, and Bioinformatics  
In the second step, only those fold models belonging to the determined structural class are selected for the final fold prediction.  ...  In the first step of the triage method, the most probable structural class is predicted using a set of manually constructed, high-level, generalized structural HMMs that represent seven general protein  ...  ACKNOWLEDGMENTS We thank Jadwiga Bienkowska for her helpful discussions about the model construction and Robert Rogers, Jr., for setting up and maintaining the web server.  ... 
doi:10.1002/prot.10194 pmid:12211033 fatcat:ubkspdktzneqvawwv55kyqjaje

Deep localization of protein structures in fluorescence microscopy images [article]

Muhammad Tahir, Saeed Anwar, Ajmal Mian, Abdul Wahab Muzaffar
2021 arXiv   pre-print
Accurate localization of proteins from fluorescence microscopy images is challenging due to the inter-class similarities and intra-class disparities introducing grave concerns in addressing multi-class  ...  The proposed deep pipeline can better guide drug designing procedures in the pharmaceutical industry and open new avenues for researchers in computational biology and bioinformatics.  ...  Our method provides the best results due to the correct identification of proteins present in the images.  ... 
arXiv:1910.04287v3 fatcat:dzkjwvrbbfgodhstfis6ja6p7e

Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

A. Pipier, A. Devaux, T. Lavergne, A. Adrait, Y. Couté, S. Britton, P. Calsou, J. F. Riou, E. Defrancq, D. Gomez
2021 Scientific Reports  
In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures.  ...  In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins.  ...  The Nanobio-ICMG platform (UAR 2607) is acknowledged for providing facilities for the synthesis and purification of oligonucleotides (R. Lartia) as well as for mass spectrometry analyses (A.  ... 
doi:10.1038/s41598-021-92806-8 pmid:34188089 fatcat:jzrqk6p7nnbvzfvcsdtf3gsucq
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