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Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

Phineus R. L. Markwick, Carla F. Cervantes, Barrett L. Abel, Elizabeth A. Komives, Martin Blackledge, J. Andrew McCammon
2010 Journal of the American Chemical Society  
years, considerable effort has been focused on improving the interpretation of such NMR observables, including the effect of dynamic averaging: focusing predominantly on RDC data, simultaneous structure-dynamics  ...  by the fact that this experimental observable represents both an ensemble and time average.  ...  by the fact that this experimental observable represents both an ensemble and time average.  ... 
doi:10.1021/ja9093692 pmid:20063881 pmcid:PMC2812018 fatcat:onyzlpxabvh6bh5rqjf7pxkldi

An Experimental Study of LP-Based Approximation Algorithms for Scheduling Problems

Martin W. P. Savelsbergh, R. N. Uma, Joel Wein
2005 INFORMS journal on computing  
In this setting as well, the techniques yield algorithms with improved performance; we give the best-known solutions for a set of instances provided by BASF AG, Germany.  ...  We study both the quality of lower bounds given for this problem by different linearprogramming relaxations and combinatorial relaxations, and the quality of upper bounds delivered by a number of approximation  ...  Savelsbergh's research was partially supported by NSF Grant DMI-9410102. R. N. Uma's research was partially supported by NSF Grant CCR-9626831 and NSF Grant DMI-9970063.  ... 
doi:10.1287/ijoc.1030.0055 fatcat:duyan3aqebhifgrbs77nmonaeq

Storm-Relative Observations in Tropical Cyclone Data Assimilation with an Ensemble Kalman Filter

Altuğ Aksoy
2013 Monthly Weather Review  
Spatially smoother analyses are obtained in the horizontal, and the evolution of the azimuthally averaged wind structure during short-range forecasts demonstrates better consistency with the nature run  ...  The use of the storm-relative observations with a more homogeneous spatial distribution also reveals that a reduction of the covariance localization horizontal length scale by ½ to ;120 km provides the  ...  The author acknowledges funding from the NOAA Hurricane Forecast Improvement Project that supported this work.  ... 
doi:10.1175/mwr-d-12-00094.1 fatcat:sokzlxkbi5gxlbsrjmvq4cwdve

Classifying land development in high-resolution Satellite imagery using hybrid structural-multispectral features

C. Unsalan, K.L. Boyer
2004 IEEE Transactions on Geoscience and Remote Sensing  
We also implement and test a probabilistic relaxation algorithm followed by the maximum a priori decision rule.  ...  This paper addresses the novel combination of these types of features (hybrids) by using the structural features, straight line support regions based on gradient orientation, as cue regions for multispectral  ...  The Bayes classifier assumes a parametric model for the data distribution, typically Gaussian. If the data represent a Gaussian type distribution, the classifier performs well.  ... 
doi:10.1109/tgrs.2004.835224 fatcat:reeppbnpxzb3tfp7nycwqqtkyu

Crystal Structure Search with Random Relaxations Using Graph Networks [article]

Gowoon Cheon, Lusann Yang, Kevin McCloskey, Evan J. Reed, Ekin D. Cubuk
2020 arXiv   pre-print
Many properties of a material are determined by its atomic crystal structure.  ...  Surprisingly, we find that data augmentation of adding Gaussian noise improves both the accuracy and out of domain generalization of our models.  ...  Figure 2 : 2 Force(left) and stress(right) distribution of random structure relaxations data.  ... 
arXiv:2012.02920v2 fatcat:igb5k4x34ne7hcsnbh6ahkp2te

Brief Announcement

Adones Rukundo, Aras Atalar, Philippas Tsigas
2018 Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18  
Semantics relaxation has the potential to reach monotonically very high throughput by continuously trading relaxation for throughput. Previous solutions could not fully leverage this potential.  ...  We briefly describe an efficient lock-free concurrent stack design with tunable and tenable relaxed semantics to allow for better performance.  ...  INTRODUCTION To improve performance scalability of concurrent data structures, recent research has focused on expanding the set of legal behaviours, including; weakening consistency and semantic relaxation  ... 
doi:10.1145/3212734.3212794 fatcat:h6a7egngn5eyxccnvfap7vgvcy

The Open Catalyst 2020 (OC20) Dataset and Community Challenges [article]

Lowik Chanussot, Abhishek Das, Siddharth Goyal, Thibaut Lavril, Muhammed Shuaibi, Morgane Riviere, Kevin Tran, Javier Heras-Domingo, Caleb Ho, Weihua Hu, Aini Palizhati, Anuroop Sriram (+5 others)
2021 arXiv   pre-print
We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses.  ...  In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results.  ...  (B) Predicting relaxed structure from initial structure (IS2RS ) as evaluated by Average Distance within Threshold (ADwT).  ... 
arXiv:2010.09990v4 fatcat:f73sln2mnvhrnh3hagipztkb6y

Time-averaging crystallographic refinement: possibilities and limitations using α-cyclodextrin as a test system

C. A. Schiffer, P. Gros, W. F. van Gunsteren
1995 Acta Crystallographica Section D: Biological Crystallography  
Three resolution ranges of the data are used, the memory relaxation time of the averaging is varied, and several overall temperature factors are used.  ...  The method of time-averaging crystallographic refinement is assessed using a small molecule, a-cyclodextrin, as a test system. A total of 16 refinements are performed on simulated data.  ...  distribution by an MDgenerated ensemble of protein structures.  ... 
doi:10.1107/s0907444994007158 pmid:15299339 fatcat:wwqydu7ufjgotjmloy4v2ehw3i

Relaxation of backbone bond geometry improves protein energy landscape modeling

Patrick Conway, Michael D. Tyka, Frank DiMaio, David E. Konerding, David Baker
2013 Protein Science  
We performed large-scale explorations of the energy landscapes of 82 protein domains under each model, and find that the introduction of bond angle flexibility significantly increases the average energy  ...  These results suggest that backbone bond angle relaxation makes an important contribution to native structure energetics, that current energy functions are sufficiently accurate to capture the energetic  ...  For each FastRelax cycle, we computed the average final energy and elapsed time from start. The relax protocols were performed for 400 s.  ... 
doi:10.1002/pro.2389 pmid:24265211 pmcid:PMC3892298 fatcat:ekkusgflxnes3onsvbxwu4lhc4

Distributed Structural Relaxation of XPath Queries

Georgia Koloniari, Evaggelia Pitoura
2009 Proceedings / International Conference on Data Engineering  
Due to the structural heterogeneity of XML, queries are often interpreted approximately. This is achieved by relaxing the query and ranking the results based on their relevance to the original query.  ...  To process such queries efficiently, we propose using a distributed clustered index to group documents based on their structural similarity.  ...  DISCUSSION AND EXTENSIONS The main claim of this paper is that clustering improves the performance of relaxation over distributed data collections.  ... 
doi:10.1109/icde.2009.110 dblp:conf/icde/KoloniariP09 fatcat:d5g42ebdnrgwdizaq3plwxcvni

Efficient Sampling in Fragment-Based Protein Structure Prediction Using an Estimation of Distribution Algorithm

David Simoncini, Kam Y. J. Zhang, Yang Zhang
2013 PLoS ONE  
This iteratively-refined distribution is used to guide the selection of fragments during the building of models for subsequent rounds of structure prediction.  ...  We observed an improvement in energy-driven blind selection of models on a benchmark of 20 in comparison with the Rosetta AbInitioRelax protocol.  ...  EdaFold CG is a dataset of models obtained by generating coarse-grained EdaFold CG followed by Rosetta's fast Relax protocol.  ... 
doi:10.1371/journal.pone.0068954 pmid:23935913 pmcid:PMC3723781 fatcat:al4idfdwibby7gaouqbkba2h7i

A Novel Algorithm For Radar Target Feature Extraction

Shen Limin, Changde Lu, Xuesheng Pei, Jianning Su
2018 MATEC Web of Conferences  
based on the SVM classifier show that the novel feature extraction method can improve recognition performances greatly .  ...  The new algorithm mainly extracts the features of the effective distance unit according to the distribution of the target scattering points to improve the recognition efficiency.The experimental results  ...  Relax algorithm is a nonlinear least squares relaxation algorithm for solving simple scattering point model parameters.In this paper, by using the average distance of the Relax algorithm for radar echo  ... 
doi:10.1051/matecconf/201817601027 fatcat:tbgcwk45lzacncmupwb6xbm5au

Influence of interstitial Mn on local structure and magnetism inMn1+δSb

Joshua A. Kurzman, Andrew J. Martinolich, James R. Neilson
2015 Physical Review B  
We report x-ray total scattering and pair distribution function (PDF) studies of the structural relaxation around interstitial manganese (Mn$_i$) in ferromagnetic Mn$_{1+\delta}$Sb ($0.03 \le \delta \le  ...  Such structural relaxation increases the DFT calculated moment on Mn$_i$, which aligns antiparallel to the primary Mn moments, but leads to insubstantial changes in the average Mn and Sb moments and moments  ...  Borkiewicz for assistance collecting total scattering data, and the instrument scientists at 11-BM for powder diffraction data acquisition.  ... 
doi:10.1103/physrevb.92.184414 fatcat:ki5gf7sn2fgptg6e443cb7npoi

On the Relationship Between Combinatorial and LP-Based Approaches to NP-Hard Scheduling Problems [chapter]

R. N. Uma, Joel Wein
1998 Lecture Notes in Computer Science  
As a result we obtain the rst worst-case analysis of the quality of the lower bound delivered by these combinatorial relaxations.  ...  We observe that on most kinds of synthetic data used in experimental studies a simple heuristic, used in successful combinatorial branch-and-bound algorithms for the problem, outperforms on average all  ...  Some of the results in Section 3 were independently obtained by David Williamson and a joint journal paper is forthcoming.  ... 
doi:10.1007/3-540-69346-7_30 fatcat:mf7ha72jkrfufegjkl6zrvk4qm

Sub-cellular force microscopy in single normal and cancer cells

H. Babahosseini, B. Carmichael, J.S. Strobl, S.N. Mahmoodi, M. Agah
2015 Biochemical and Biophysical Research Communications - BBRC  
, and the relaxation time of sub-cellular structures.  ...  The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity  ...  Acknowledgements The research is funded by the National Science Foundation under award number CBET-1403304 and ECCS-0925945 (to MA), and the University of Alabama RGC award (to SNM).  ... 
doi:10.1016/j.bbrc.2015.05.100 pmid:26036579 fatcat:bq4jdrf4izaxxewoki4xbwza7m
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