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Neural Upscaling from Residue-level Protein Structure Networks to Atomistic Structure [article]

Vy Duong, Elizabeth Diessner, Gianmarc Grazioli, Rachel W. Martin, Carter T. Butts
2021 arXiv   pre-print
Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs.  ...  These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates  ...  Acknowledgments: We thank Ray Luo for co-advising of Vy Duong and use of computational resources. This research was also supported by computational resources supported by UCI Calit2 Think Tank.  ... 
arXiv:2109.06700v1 fatcat:z4wl5wevizgc7hvr32dbimc6yu

Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Vy T. Duong, Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, Carter T. Butts
2021 Biomolecules  
Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs.  ...  These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates  ...  Acknowledgments: We thank Ray Luo for co-advising of Vy Duong and use of computational resources. This research was also supported by computational resources supported by UCI Calit2 Think Tank.  ... 
doi:10.3390/biom11121788 pmid:34944432 pmcid:PMC8698800 fatcat:24phbmpo2zgtbgdhvvoefjhx6e

High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

Ye Tian, Charles D. Schwieters, Stanley J. Opella, Francesca M. Marassi
2016 Journal of Biomolecular NMR  
The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules.  ...  Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely  ...  This research was supported by a grant from the National Institutes of Health (GM118186) and by the Resource for Molecular Imaging of Proteins at UCSD supported by the National Institutes of Health (P41  ... 
doi:10.1007/s10858-016-0082-5 pmid:28035651 pmcid:PMC5487259 fatcat:noxc6xisfzezlc33fsttqjauyq

Modification of Calcium Carbonate and Calcium Oxalate Growth Morphology and Kinetics by Carboxyl-rich Biomolecules(Crystal Growth and Chirality)

James J. De Yoreol, Patricia M. Dove, Andrzej Wierzbicki, John R. Hoyer
2008 Journal of the Japanese Association for Crystal Growth  
lhe infiuence of biornolecules on crysta1lization in living systems leads to dramatic control ever crystal shapes, grewth rates and propenies.  ...  Here we illustrate these factors using exaniples from the calcite and calcium oxalate monohydrate systems, in which carboxyl-rich biomolecules are usecl to infiuence growth.  ...  This work was supported by awards to JDY from the Department of Energy' $ Othce of Basic Energy Sciences and grants DK61673 and DK33501 from the National Institutes of Health.  ... 
doi:10.19009/jjacg.35.1_24 fatcat:rjkdwndvbjhhhfz5fvv2qd7flq

Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method

Asim Okur, Benjamin T. Miller, Keehyoung Joo, Jooyoung Lee, Bernard R. Brooks
2013 Journal of Chemical Theory and Computation  
However, for larger and more complicated systems, the use of T-REM is computationally intensive since the complexity of the free energy landscape and number of replicas required increase with system size  ...  CSA uses a genetic algorithm to generate a diverse set of conformations to determine the minimum energy structure.  ...  We also would like to thank Rich Pastor and Michael Shirts for useful discussions.  ... 
doi:10.1021/ct300996m pmid:23585739 pmcid:PMC3621806 fatcat:ibzctyzz6zfjndsus6bgrgy4fa

Exploring energy landscapes: from molecular to mesoscopic systems

Dwaipayan Chakrabarti, Halim Kusumaatmaja, Victor Rühle, David J. Wales
2014 Physical Chemistry, Chemical Physics - PCCP  
We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules.  ...  Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed.  ...  DC acknowledges support also through a Marie Curie Incoming International Fellowship from the European Commission and an Oppenheimer Research Fellowship from the University of Cambridge.  ... 
doi:10.1039/c3cp52603h pmid:24067895 fatcat:ip2hcfgkdbec3ilxflinej42om

Topology, landscapes, and biomolecular energy transport

Justin E. Elenewski, Kirill A. Velizhanin, Michael Zwolak
2019 Nature Communications  
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules.  ...  Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules.  ...  The authors declare that all data supporting the findings in this manuscript are available within the paper and its supplementary information.  ... 
doi:10.1038/s41467-019-12700-w pmid:31604949 pmcid:PMC6789131 fatcat:rrpeky3jkbcgpjry6jt7tkgdc4

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects

Elisa Fadda, Robert J. Woods
2010 Drug Discovery Today  
Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans.  ...  The current state of carbohydrate force fields is reviewed with a focus on developmental differences and applicability in the growing area of glycomimetic design.  ...  Acknowledgements The authors gratefully acknowledge the Science Foundation of Ireland (SFI) for funding (07/RP1/B1321).  ... 
doi:10.1016/j.drudis.2010.06.001 pmid:20594934 pmcid:PMC3936463 fatcat:3fxenevs6najxkmdvx4c5jq43i

A spin-1 representation for dual-funnel energy landscapes

Justin E. Elenewski, Kirill A. Velizhanin, Michael Zwolak
2018 Journal of Chemical Physics  
The interconversion between left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape.  ...  A three-state model - left, right, and unstructured - can account for most key intermediates during chiral interconversion.  ...  With this classification in hand, a relative free energy ∆G jk = −k B T log [P k /P j ] (5) may be calculated between states of populations P j and P k , respectively.  ... 
doi:10.1063/1.5036677 pmid:30037251 fatcat:wiqkkger3bg3de7bwudcwvxzva

Fundamentals of drug design from a biophysical viewpoint

Wilfred F. Van Gunsteren, Paul M. King, Alan E. Mark
1994 Quarterly Reviews of Biophysics (print)  
The total free energy of a system is thus dependent on all possible electronic and nuclear degrees of freedom. For any realistic system the absolute free energy cannot be calculated.  ...  In view of these difficulties, the calculation of the absolute free energy or entropy of a molecular system is virtually impossible.  ... 
doi:10.1017/s0033583500003103 pmid:7784540 fatcat:lmt2u53ai5asdncymlp672f5mm

Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan–protein complexes

Robert J Woods, Matthew B Tessier
2010 Current Opinion in Structural Biology  
When taken with respect to the unliganded states, these calculations can also provide insight into the entropic and enthalpic changes in free energy associated with glycan binding.  ...  Here we present a summary of the basic strategies associated with employing classical force field based modeling approaches to problems in glycoscience, with a focus on identifying typical pitfalls and  ...  Free energy difference calculations Free energy difference (FED) methods often make use of the ability to convert one ligand into another over a series of small steps along a non-physical path [24] to  ... 
doi:10.1016/j.sbi.2010.07.005 pmid:20708922 pmcid:PMC3936461 fatcat:umo5bohfbzcqxffsl4zjjcejvu

The Xplor-NIH NMR molecular structure determination package

Charles D Schwieters, John J Kuszewski, Nico Tjandra, G Marius Clore
2003 Journal of magnetic resonance (San Diego, Calif. 1997 : Print)  
We announce the availability of the Xplor-NIH software package for NMR biomolecular structure determination.  ...  In addition to many features which have been developed over the last 20 years, the Xplor-NIH package contains an interface with a new programmatic framework written in C++.  ...  In particular, the Xplor-NIH software package owes a great debt to Axel Br€ u unger as the original creator of XPLOR.  ... 
doi:10.1016/s1090-7807(02)00014-9 pmid:12565051 fatcat:z5jlzhpg4ff65b6ltcistari6i

Topology, Landscapes, and Biomolecular Energy Transport [article]

Justin E. Elenewski, Kirill A. Velizhanin, Michael Zwolak
2019 arXiv   pre-print
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules.  ...  Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules.  ...  A. V. was supported by the U.S. Department of Energy through the LANL/LDRD Program. Computing resources were  ... 
arXiv:1904.11154v1 fatcat:tqtewsdo3bgdvobus4szondawi

Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes

Shaowei Ding, Allison Cargill, Suprem Das, Igor Medintz, Jonathan Claussen
2015 Sensors  
In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer  ...  The future outlook and challenges for the research field are also detailed.  ...  able to probe and recognize biomolecular interactions in a homogeneous format [89] .  ... 
doi:10.3390/s150614766 pmid:26110411 pmcid:PMC4507682 fatcat:65neby745jbtlogiyaoy35u5ka

Novel Computational Methods to Design Protein-Protein Interactions

Alice Qinhua Zhou, Corey S. O'Hern, Lynne Regan
2014 Biophysical Journal  
Insights to these issues will provide better paradigms with which to design therapeutic mutants of PLN for treatment of heart failure, and also demonstrate a model by which an enzyme can be controlled  ...  Ammonia lyases and aminomutases are emerging as important enzymatic systems, not only in green synthetic routes to chiral amines, but also as potential target for enzyme therapeutic for treating diseases  ...  From the random ideal helix configuration, we obtained local-minimum free energy states by REM simulations and principal component analysis.  ... 
doi:10.1016/j.bpj.2013.11.3622 fatcat:v7zhjwxg3jcupbecfmbszebtii
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