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Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

Katrina W. Lexa, Heather A. Carlson
2013 Journal of Chemical Information and Modeling  
However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold.  ...  Based on comparison to crystallographic density, we previously showed that mixedsolvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent  ...  We also thank Jeanne Stuckey, Oleg Tsodikov, and Thomas Goddard for their advice and assistance in interpreting electron density data.  ... 
doi:10.1021/ci300430v pmid:23327200 pmcid:PMC3581705 fatcat:fuo5j34mt5f6jdfdwa4yga24ie

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, Klaus Schulten
2014 Acta Crystallographica Section D: Biological Crystallography  
X-ray crystallography remains the most dominant method for solving atomic structures.  ...  applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank.  ...  The authors also acknowledge the Beckman Postdoctoral Fellowship program for supporting A. Singharoy.  ... 
doi:10.1107/s1399004714013856 pmid:25195748 pmcid:PMC4157446 fatcat:gtwafca5cnewvldduh2ccull5y

Evaluation of protein surface roughness index using its heat denatured aggregates

Hrishikesh Mishra, Tapobrata Lahiri
2009 Nature Precedings  
Finally SRI for a particular protein was predicted by clustering of decisions obtained through feeding of multiple data into RBPN, to obtain general tendency of decision, as well as to discard the noisy  ...  The cluster centre of the largest cluster was found to be the best match for mapping of Surface Roughness Index of each protein in our study.  ...  Acknowledgements We are thankful to MHRD Author contributions  ... 
doi:10.1038/npre.2009.3693.1 fatcat:gxqo6civ4fbdhmsp6guzgsj2di

Probabilistic ensembles for improved inference in protein-structure determination

Ameet Soni, Jude Shavlik
2011 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11  
Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography.  ...  Protein X-ray crystallography À À À the most popular method for determining protein structures À À À remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality  ...  ACMI and the data set of experimentally-phased density maps is available online at http://www.cs.wisc.edu/acmi/.  ... 
doi:10.1145/2147805.2147834 dblp:conf/bcb/SoniS11 fatcat:jtcklfqddffcbde26lcrhsizwa

PROBABILISTIC ENSEMBLES FOR IMPROVED INFERENCE IN PROTEIN-STRUCTURE DETERMINATION

AMEET SONI, JUDE SHAVLIK
2012 Journal of Bioinformatics and Computational Biology  
Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography.  ...  Protein X-ray crystallography À À À the most popular method for determining protein structures À À À remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality  ...  ACMI and the data set of experimentally-phased density maps is available online at http://www.cs.wisc.edu/acmi/.  ... 
doi:10.1142/s0219720012400094 pmid:22809310 pmcid:PMC3401969 fatcat:hjitaepuezbero7esjnsfduhae

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Ashutosh Srivastava, Tetsuro Nagai, Arpita Srivastava, Osamu Miyashita, Florence Tama
2018 International Journal of Molecular Sciences  
Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures.  ...  Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/ijms19113401 fatcat:vojdzjsg75hgdohna6bjx7vjky

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

Brandon Frenz, Sebastian Rämisch, Andrew J. Borst, Alexandra C. Walls, Jared Adolf-Bryfogle, William R. Schief, David Veesler, Frank DiMaio
2019 Structure  
However, existing protocols for the refinement of glycoproteins at low resolution have failed to keep up with these advances.  ...  We benchmarked this approach using 12 crystal structures and showed that glycan geometries can be automatically improved while maintaining good fit to the crystallographic data.  ...  Acknowledgements Research reported in this publication was supported by the National Institute of General Medical Sciences (R01GM120553 to D.V., R01GM123089 to F.D., T32GM008268 to A.J.B. and A.C.W.),  ... 
doi:10.1016/j.str.2018.09.006 pmid:30344107 pmcid:PMC6616339 fatcat:pe6hfiiwubby7lgv6ruubbxr6y

Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G. Mayne, Semin Lee, Chun-Hsing Chen, Adam Zlotnick, Klaus Schulten, Amar H. Flood
2015 Journal of the American Chemical Society  
Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies. Singharoy et al.  ...  restraints, even at a very high diffraction data resolution of 0.84 Å.  ...  Maren Pink for helpful discussions. A.S., C.G.M. and K.S. acknowledge support from the National Institutes of Health (NIH; 9P41GM104601, 5R01GM098243-02 and U54GM087519).  ... 
doi:10.1021/jacs.5b04407 pmid:26121416 pmcid:PMC4504762 fatcat:7orx7tl2pjhafp7vmsxhvhgjjq

The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years

Marek Grabowski, Marcin Cymborowski, Przemyslaw J. Porebski, Tomasz Osinski, Ivan G. Shabalin, David R. Cooper, Wladek Minor
2019 Structural Dynamics  
in improving previously determined protein structures.  ...  In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing  ...  ACKNOWLEDGMENTS We thank all the people who have contributed data to IRRMC and provided us with helpful feedback.  ... 
doi:10.1063/1.5128672 pmid:31768399 pmcid:PMC6874509 fatcat:mrybrapyxzdwxgfkerixesg3im

High-Throughput Protein Crystallography

A AZARANI, B SEGELKE, D TOPPANI, T LEKIN
2006 Journal of the Association for Laboratory Automation  
It appears fair to say that protein crystallography in general has made significant technical progress through increased public and commercial funding devoted to the development of high throughput technologies  ...  Given that no special marker atoms need to be introduced into the protein, the method is likely to gain rapid acceptance in high throughout crystallography (see Matthews (52) for a review about SAD data  ...  Additional phasing experiments need to be carried out to obtain the missing phases.  ... 
doi:10.1016/j.jala.2005.09.004 fatcat:45ix6vuq5zakbdyvbgc77o5e3u

Au or FeS2? Validation of protein models and refinement protocols

G. J. Kleywegt, T. A. Jones
1996 Acta Crystallographica Section A Foundations of Crystallography  
At the e11d of a cycle REFMAC also w1ites weighted map coefficients to give less biased maps for rebuilding, taking care to restore missing data.  ...  is generally improved by refining it to improve agreement with the observed diffraction data.  ... 
doi:10.1107/s0108767396095712 fatcat:645lwotv3naihgyq4tmk6y32pa

Atomic model building and refinement into high-resolution cryo-EM maps

Bruno Klaholz, S. Kundhavai Natchiar, Alexander Myasnikov, Hanna Kratzat, Isabelle Hazemann, Bruno Klaholz
2017 Protocol Exchange  
Here we present a generally applicable protocol for atomic model building and refinement into high-resolution cryo-EM maps, which in addition includes the refinement of nucleotides and amino acids with  ...  In the accompanying paper to this protocol, we describe the high-resolution structure of the human ribosome, which includes numerous chemical modifications.  ...  Acknowledgements We thank Jonathan Michalon, Remy Fritz and Romaric David for IT support.  ... 
doi:10.1038/protex.2017.122 fatcat:v5oxfrmasvdpvbhhlem2ncb4lu

Report of a workshop on the use of statistical validators in protein X-ray crystallography

E. Dodson, G. J. Kleywegt, K. Wilson
1996 Acta Crystallographica Section D: Biological Crystallography  
Improvement in refinement possibilities for proteins Data quality There has been a general improvement in the quality of diffraction data obtained over the past five years.  ...  There is so far no requirement or proper mechanism for reporting experimental data quality in the data bank. mmCIF will address this need.  ... 
doi:10.1107/s0907444995010638 pmid:15299755 fatcat:2xrgyl6ajjhn3geopsa66c7lla

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Zhao Wang, Corey F. Hryc, Benjamin Bammes, Pavel V. Afonine, Joanita Jakana, Dong-Hua Chen, Xiangan Liu, Matthew L. Baker, Cheng Kao, Steven J. Ludtke, Michael F. Schmid, Paul D. Adams (+1 others)
2014 Nature Communications  
We used the map to derive an all-atom model with a newly implemented real-space optimization protocol.  ...  The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps.  ...  Acknowledgements This work was supported by the National Institutes of Health through grants (P41GM103832 and R01GM079429 to W.C.; R44GM103417 to B.B.; R01AI090280 to  ... 
doi:10.1038/ncomms5808 pmid:25185801 pmcid:PMC4155512 fatcat:s57gw3wmivdhbo447qa4s4k7xi

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments

Yifei Qi, Jumin Lee, Abhishek Singharoy, Ryan McGreevy, Klaus Schulten, Wonpil Im
2016 Journal of Physical Chemistry B  
Atomic structures are derived through the fitting and refinement of an initial model into electron density maps constructed by both experiments.  ...  X-ray crystallography and cryo-electron microscopy are two popular methods for the structure determination of biological molecules.  ...  The authors also acknowledge the Beckman Postdoctoral Fellowship program for supporting A Singharoy.  ... 
doi:10.1021/acs.jpcb.6b10568 pmid:27936734 pmcid:PMC5398930 fatcat:q5fbub6afbev5dnv4kixyx4gwi
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