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Energetics of protein–DNA interactions

Jason E. Donald, William W. Chen, Eugene I. Shakhnovich
2007 Nucleic Acids Research  
In the process, we find that the results of these knowledge-based potentials show a strong dependence on the interaction distance and the derivation method.  ...  Finally, we present a knowledge-based potential that gives comparable or superior results to the best of the other methods, including the molecular mechanics force field AMBER99.  ...  We would also like to thank Chi Zhang, Song Liu, Qianqian Zhu, and Yaoqi Zhou and Alexandre Morozov, James Havranek, David Baker, and Eric Siggia for making, respectively, their ÁG and ÁÁG data freely  ... 
doi:10.1093/nar/gkl1103 pmid:17259221 pmcid:PMC1851630 fatcat:h7jf3qqzfjgzfjco2jr4tjrfdy

A distance-dependent atomic knowledge-based potential for improved protein structure selection

Hui Lu, Jeffrey Skolnick
2001 Proteins: Structure, Function, and Bioinformatics  
A heavy atom distance-dependent knowledge-based pairwise potential has been developed.  ...  Examination of the z-scores for individual pairwise distance shells indicates that the specificity for the native protein structure is greatest at pairwise distances of 3.5-6.5 Å, i.e., in the first solvation  ...  IV Comparison of Atomic Knowledge-Based Potential and Residue-Based Potentials for Sequences from the Fischer Database: Comparison of the Lowest-Energy Structures Picked byDifferent Potentials* Atomic  ... 
doi:10.1002/prot.1087 pmid:11455595 fatcat:pkr4mhm7wfdwdj5kekouhlrzgq

Single-sequence protein structure prediction using supervised transformer protein language models [article]

Wenkai Wang, Zhenling Peng, Jianyi Yang
2022 bioRxiv   pre-print
The sequence embedding is fed into a multi-scale network with knowledge distillation to predict inter-residue 2D geometry, including distance and orientations.  ...  It remains challenging for single-sequence protein structure prediction with AlphaFold2 and other deep learning methods.  ...  To the best of our knowledge, RGN2 is the first reported deep learning-based single-sequence method for 3D structure prediction 16 .  ... 
doi:10.1101/2022.01.15.476476 fatcat:zfbeu6drbvh4hjjq2cxwksq5be

Symbol Extraction Method and Symbolic Distance for Analysing Medical Time Series [chapter]

Fernando Alonso, Loïc Martínez, Aurora Pérez, Agustín Santamaría, Juan Pedro Valente
2006 Lecture Notes in Computer Science  
This paper focuses on the process of transforming numerical time series into a symbolic domain and on the definition of both this domain and a distance for comparing symbolic temporal sequences.  ...  Most of the approaches that address this problem are based on numerical algorithms that calculate distances, clusters, index trees, etc.  ...  Transposition-based distances use the transposition of the sequence elements.  ... 
doi:10.1007/11946465_28 fatcat:6kbcw625ebf3dj53n7ydpaglee

Software Knowledge Entity Relation Extraction with Entity-Aware and Syntactic Dependency Structure Information

Mingjing Tang, Tong Li, Wei Wang, Rui Zhu, Zifei Ma, Yahui Tang, Francisco Ortin
2021 Scientific Programming  
Semantic relation extraction of software knowledge entities is a critical task for software knowledge graph construction, which has an important impact on knowledge graph based tasks such as software document  ...  Software knowledge community contains a large scale of software knowledge entities with complex structure and rich semantic relations.  ...  Wei Wang and Yahui Tang provided comments for revision. All authors reviewed and edited the manuscript, and all of them read and approved the final manuscript.  ... 
doi:10.1155/2021/7466114 fatcat:nfisztyw75dnrk46mwc6uczmwq

Word Sense Disambiguation-based Sentence Similarity

ChukFong Ho, Masrah Azrifah Azmi Murad, Rabiah Abdul Kadir, Shyamala C. Doraisamy
2010 International Conference on Computational Linguistics  
This is achieved by transforming an existing most-outstanding corpus-based measure into a knowledge-based measure, which is then integrated with word sense disambiguation.  ...  This paper presents a method which computes the similarity between two sentences based on a comparison of their actual meanings.  ...  In comparison, knowledge-based methods compute the similarity between two sentences based on the semantic information collected from knowledge bases.  ... 
dblp:conf/coling/HoMKD10 fatcat:vawz3pwe5bbcpd77oy4i4avhym

Towards Lifelong Learning and Organization of Whole Body Motion Patterns [chapter]

Dana Kulić, Wataru Takano, Yoshihiko Nakamura
2010 Springer Tracts in Advanced Robotics  
The model size is adaptable based on the discrimination requirements in the associated region of the current knowledge base.  ...  As new motion patterns are observed, they are incrementally grouped together based on their relative distance in the model space.  ...  Acknowledgment This work is supported by the Japanese Society for the Promotion of Science grant 18.06754 and Category S Grant-in-Aid for Scientific Research 15100002.  ... 
doi:10.1007/978-3-642-14743-2_8 fatcat:5uqepixe6baqxiiw3lbs5go7ve

Human action recognition from a single clip per action

Weilong Yang, Yang Wang, Greg Mori
2009 2009 IEEE 12th International Conference on Computer Vision Workshops, ICCV Workshops  
We also present a method for learning a transferable distance function for these patches.  ...  The transferable distance function learning extracts generic knowledge of patch weighting from previous training sets, and can be applied to videos of new actions without further learning.  ...  Patch based Action Comparison We compute the distance between two video clips by comparing the patches from both clips.  ... 
doi:10.1109/iccvw.2009.5457663 dblp:conf/iccvw/Yang0M09 fatcat:6ib727kbu5f5ddwsgozikmudhy

Pattern recognition and probabilistic measures in alignment-free sequence analysis

I. Schwende, T. D. Pham
2013 Briefings in Bioinformatics  
With the massive production of genomic and proteomic data, the number of available biological sequences in databases has reached a level that is not feasible anymore for exact alignments even when just  ...  However, alignments are still the standard method for real world applications in biological sequence analysis, and the time efficient alignment-free approaches are usually applied in cases when the accustomed  ...  [12] sequence Mahalanobis distance, comparison Kullback^Leibler discrep- ancy, Cosine distance and USM-based discrepancy D2z distance Implementation for Kantorovitz  ... 
doi:10.1093/bib/bbt070 pmid:24096012 fatcat:oa5q7vx2vjfardq4lokqgscyyy

Reading Scanpaths

Barbara Rösch, Rainer Hammwöhner
2015 Zenodo  
Method: We applied string distance measures and cluster analysis to investigate scanpath sequences, fixation times and the distribution of the visual attention.  ...  Results: Despite encountering difficulties in comparing scanpaths, there are indications that the users' knowledge influences their gaze patterns.  ...  The values computed by the Levenshtein distance for each pairwise scanpath comparison can be transformed in a distance matrix.  ... 
doi:10.5281/zenodo.17962 fatcat:4t2ebsyyvvc47oqx66tnpli6je

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

H. A. Scheraga, S. Rackovsky
2014 Proceedings of the National Academy of Sciences of the United States of America  
Significance A Fourier-based sequence distance function for proteins is presented, which exhibits high accuracy in structural homology searches.  ...  Essentially, all current methods for sequence comparison, which provide the framework in which these difficulties arise, are based on alignment techniques.  ...  We are not aware of any studies that investigate this point for alignmentbased sequence comparison, or superposition-based structural comparison methods.  ... 
doi:10.1073/pnas.1403599111 pmid:24706836 pmcid:PMC3986189 fatcat:d6r3oo4sn5grfhy5citmm6p67i

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures

RyangGuk Kim, Jun-tao Guo
2009 BMC Genomics  
In addition, current approaches to comparison of protein-DNA complexes are mainly based on protein sequence similarity while the DNA sequences are not taken into account.  ...  Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation.  ...  Acknowledgements The authors thank the anonymous reviewers for many helpful comments on the manuscript.  ... 
doi:10.1186/1471-2164-10-s1-s13 pmid:19594872 pmcid:PMC2709256 fatcat:tmnrq4425bacxphhwqxfsimanm

An Expert System for Quality Assurance of Document Image Collections [chapter]

Roman Graf, Reinhold Huber-Mörk, Alexander Schindler, Sven Schlarb
2012 Lecture Notes in Computer Science  
We employ artificial intelligence technologies (i.e. knowledge base, expert rules) to emulate reasoning about the knowledge base similar to a human expert.  ...  A statistical analysis of the automatically extracted information from the image comparison tool and the qualitative analysis of the aggregated knowledge are presented.  ...  An expert system comprises the inference engine that is employed for reasoning about the knowledge base. The knowledge base contains expert knowledge in form of data or rules.  ... 
doi:10.1007/978-3-642-34234-9_25 fatcat:3bxk326bynervoasg3n3slgfzq

Implicit Learning of Musical Timbre Sequences: Statistical Regularities Confronted With Acoustical (Dis)Similarities

Barbara Tillmann, Stephen McAdams
2004 Journal of Experimental Psychology. Learning, Memory and Cognition  
sequence.  ...  7 For direct comparisons with Johnson and Jusczyk (2001) , this new timbre material that included accent patterns should be defined in such a way that both triplets and part-triplets occur in the exposition  ...  the listeners would be unlikely to have such knowledge for these sounds and sequences.  ... 
doi:10.1037/0278-7393.30.5.1131 pmid:15355141 fatcat:t23f7jdds5htjpwma6ccny5u3u

A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction

Mridu Gupta, Shailendra Singh
2012 International Journal of Computer Applications  
The K-tuple distance approach is not effective for set of sequences which are almost identical where as F-tuple distance is useful for constructing phylogenetic tree for set of identical sequences.  ...  Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution.  ...  Phylogenetics is useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution [2] .  ... 
doi:10.5120/8229-1303 fatcat:anz63ighsvfs7mil2itmq6alae
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