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Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes

G. E. Sims
2003 Nucleic Acids Research  
A global conformational space of 6253 dinucleoside monophosphate (DMP) units consisting of RNA and DNA (free and protein/drug-bound) was'mapped' using high resolution crystal structures cataloged in the  ...  The mapping of the conformational space reveals nine primary clusters which distinguish among the common A-, B-and Z-forms and their various substates, plus ®ve secondary clusters for kinked or bent structures  ...  We are grateful for the support of the National Science Foundation (DBI-0114707), the National Institute of Health for a training grant for G.E.S.  ... 
doi:10.1093/nar/gkg750 pmid:14500824 pmcid:PMC206451 fatcat:cqxdgtqoorattnjfdprllntbza

Conformal and Low-Rank Sparse Representation for Image Restoration

Jianwei Li, Xiaowu Chen, Dongqing Zou, Bo Gao, Wei Teng
2015 2015 IEEE International Conference on Computer Vision (ICCV)  
In this paper, we propose a novel sparse representation approach called conformal and low-rank sparse representation (CLRSR) for image restoration problems.  ...  To achieve a more compact and representative dictionary, conformal property is introduced by preserving the angles of local geometry formed by neighboring samples in the feature space.  ...  We thank the reviewers for their valuable feedback. This work is supported in part by grants from NSFC (61325011) & (61421003), 863 Program (2013AA013801), and SRFDP (20131102130002).  ... 
doi:10.1109/iccv.2015.35 dblp:conf/iccv/LiCZGT15 fatcat:43chodi3nfhqbesvymneacx45i

Focused conformational sampling in proteins

Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
2017 Journal of Chemical Physics  
., by a grant from the Platform for Advanced Scientific Computing (PASC "Scalable Advanced Sampling in Molecular  ...  Thus, the approach is prone to underestimate local metastability due to different processes contributing to conformational drift.  ...  of signals through structural changes and binding/unbinding processes, or the disorderto-order transition of molecular recognition features. 89 It is important to realize that PIGS works as long as  ... 
doi:10.1063/1.4996879 pmid:29166086 fatcat:4qdk77dkbng4toxn325px7ivgu

Conformational activation of ADAMTS13

Kieron South, Brenda M. Luken, James T. B. Crawley, Rebecca Phillips, Mari Thomas, Richard F. Collins, Louis Deforche, Karen Vanhoorelbeke, David A. Lane
2014 Proceedings of the National Academy of Sciences of the United States of America  
Electron microscopy demonstrated a "closed" conformation of WT ADAMTS13 and suggested a more "open" conformation for GoF ADAMTS13.  ...  Thus, conformational changes in VWF are essential for its efficient cleavage by ADAMTS13.  ...  Nicoletta Sorvillo (Sanquin-AMC Landsteiner Laboratory) for providing the II-1 mAb, and Dr. Marie Scully (University College London) for providing the TTP patient plasma sample.  ... 
doi:10.1073/pnas.1411979112 pmid:25512499 pmcid:PMC4284544 fatcat:vud43ccvgbgtbc4fg65cvbxnza

Discovering Conformational Sub-States Relevant to Protein Function

Arvind Ramanathan, Andrej J. Savol, Christopher J. Langmead, Pratul K. Agarwal, Chakra S. Chennubhotla, Giuseppe Chirico
2011 PLoS ONE  
In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function.  ...  However, low populations in these sub-states and the transient nature of conformational transitions between these substates present significant challenges for their identification and characterization.  ...  Daniel Zuckerman for insightful comments on early drafts of this paper. The authors would like to thank Dr. Ivet Bahar for constructive comments during the design of this study.  ... 
doi:10.1371/journal.pone.0015827 pmid:21297978 pmcid:PMC3030567 fatcat:qgogjerzcfcbfo56taryhxo3xi

Conformal Embedding Analysis with Local Graph Modeling on the Unit Hypersphere

Yun Fu, Ming Liu, Thomas S. Huang
2007 2007 IEEE Conference on Computer Vision and Pattern Recognition  
We present the Conformal Embedding Analysis (CEA) for feature extraction and dimensionality reduction.  ...  Incorporating both conformal mapping and discriminating analysis, CEA projects the high-dimensional data onto the unit hypersphere and preserves intrinsic neighbor relations with local graph modeling.  ...  It shows that CEA provides a significant improvement for face recognition accuracy with comparative low dimensional feature representations.  ... 
doi:10.1109/cvpr.2007.383410 dblp:conf/cvpr/FuLH07 fatcat:tgeqabld3nh5hn6bgrjuh57gg4

Conformal predictions in multimedia pattern recognition

Vineeth N Balasubramanian
2011 ACM SIGMultimedia Records  
(or distance metric) for optimal and accurate conformal predictors; (ii) Validation of the calibration properties of the CP framework when applied to multi-classifier (or multi-regressor) fusion; and  ...  The fields of pattern recognition and machine learning are on a fundamental quest to design systems that can learn the way humans do.  ...  Concatenating the features from the individual blocks yielded the global feature vector for the entire image.  ... 
doi:10.1145/2069196.2069202 fatcat:pptvfth4bffxtllc3m665qodze

ELM Regime Classification by Conformal Prediction on an Information Manifold

Aqsa Shabbir, Geert Verdoolaege, Jesus Vega, Andrea Murari
2015 IEEE Transactions on Plasma Science  
The method is applied to the classification of regimes characterized by different types of edge-localized modes based on measurements of global parameters and their error bars.  ...  In this work, a distance-based conformal predictor classifier integrated with a geometricprobabilistic framework is presented.  ...  In this paper a computationally efficient nearest-neighbor CP coupled with the geometric-probabilistic data representation framework is deployed for classification of H-mode plasma regimes into H-mode  ... 
doi:10.1109/tps.2015.2489689 fatcat:3i6kuaqi3vfzxkftiildmi2ytu

Conformational flexibility of N-glycans in solution studied by REMD simulations

Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita
2012 Biophysical Reviews  
The results support the concept of "conformer selection" in protein-glycan recognition.  ...  One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein.  ...  We also thank the RIKEN Integrated Cluster of Clusters (RICC) for providing computational resources. Conflict of interest None  ... 
doi:10.1007/s12551-012-0090-y pmid:28510079 pmcid:PMC5418406 fatcat:nhecagstabhdfgplb7te3chedu

Conformational heterogeneity of the calmodulin binding interface

Diwakar Shukla, Ariana Peck, Vijay S. Pande
2016 Nature Communications  
Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity.  ...  However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood.  ...  We thank the users of the Folding@Home distributed computing project and the Blue Waters sustained-petascale computing project for providing computing time for this study.  ... 
doi:10.1038/ncomms10910 pmid:27040077 pmcid:PMC4822001 fatcat:f4wl3urcmfem7nmrs34vcbvbhm

Databases of Conformations and NMR Structures of Glycan Determinants

Anita Sarkar, Sophie Drouillard, Alain Rivet, Serge Perez
2015 Glycobiology  
The NMR ( 1 H and 13 C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats.  ...  Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to  ...  Appreciation is extended to Isabelle Jeacomine for assistance with the NMR measurements, to Alexandre Finet, Michael Reynolds and Laurence Miguet for their implications at different stages of the project  ... 
doi:10.1093/glycob/cwv054 pmid:26240168 fatcat:nmv3jxmmgja7pkuhdgh4iyglhm

Learning protein conformational space by enforcing physics with convolutions and latent interpolations [article]

Venkata K. Ramaswamy, Chris G. Willcocks, Matteo T. Degiacomi
2020 arXiv   pre-print
We present a convolutional neural network that learns a continuous conformational space representation from example structures, and loss functions that ensure intermediates between examples are physically  ...  We also show we can transfer features learnt from one protein to others, which results in superior performances, and requires a surprisingly small number of training examples.  ...  These are more computationally efficient than regular neural networks and have fewer parameters due to shared weights mimicking local connectivity in the visual cortex of the brain.  ... 
arXiv:1910.04543v2 fatcat:wcyqatq3cbhczdku5r2wwkkeqa

PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction

Gabriel Cretin, Tatiana Galochkina, Alexandre G. de Brevern, Jean-Christophe Gelly
2021 International Journal of Molecular Sciences  
In the current study, we present a new model, PYTHIA (predicting any conformation at high accuracy), for the prediction of the protein local conformations in terms of PBs directly from the amino acid sequence  ...  Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids.  ...  for this work.  ... 
doi:10.3390/ijms22168831 pmid:34445537 pmcid:PMC8396346 fatcat:5zsgh7ajtnaqlmlmctya5qlkia

The Role of Conformational Dynamics in the Recognition and Regulation of Ubiquitination

Domarin Khago, Ian J. Fucci, Robert Andrew Byrd
2020 Molecules  
These aspects involve allosteric effects and conformational dynamics that can direct recognition and chain building processes.  ...  In this review, we will describe the current state of the knowledge for conformational dynamics across a wide timescale, address the limitations of present approaches, and illustrate the potential to make  ...  Hence, there may be a recognition network operative for E2:E3 pairs that involves dynamics and allosteric shifting of conformational populations to regulate ubiquitination.  ... 
doi:10.3390/molecules25245933 pmid:33333809 fatcat:xshlacezprcs3i3jb6iwxrxc2a

Nonisometric Surface Registration via Conformal Laplace-Beltrami Basis Pursuit [article]

Stefan C. Schonsheck, Michael M. Bronstein, Rongjie Lai
2018 arXiv   pre-print
In this paper, we propose a variational model to align the Laplace-Beltrami (LB) eigensytems of two non-isometric genus zero shapes via conformal deformations.  ...  Our model is based on a novel basis pursuit scheme whereby we simultaneously compute a conformal deformation of a 'target shape' and its deformed LB eigensytem.  ...  Here we plot u where w 2 = e 2u for better visualization. From this figure we can confirm that the conformal mapping our algorithm produces is very close to the true factor.  ... 
arXiv:1809.07399v1 fatcat:ds66wdyyd5e73piws7dbf4b7ea
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