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Speeding up the drug discovery process: structural similarity searches using molecular surfaces

Dimitrios Vlachakis, Georgia Tsiliki, Dimosthenis Tsagkrasoulis, Carla Sofia Carvalho, Vasileios Megalooikonomou, Sofia Kossida
2012 EMBnet journal  
The computational load is immense, and novel innovative approaches are sought, in order to perform comprehensive structural studies and 3D searches at only a fraction of the original time required (Gerld  ...  The first task of our approach will be to calculate a set of finegrid surfaces of each protein structure available in the RCSB Protein Data Bank (Rose et al., 2011) .  ...  Rather than exploring all the 3D conformational space of large protein structures when performing docking experiments, our approach will be capable of comparing the 2D image fingerprints or 1D Fourier  ... 
doi:10.14806/ej.18.1.501 pmid:31440460 pmcid:PMC6705604 fatcat:dsia4dm35jgvpdmc7weuwayu5q

Adventures with RNA graphs

Tamar Schlick
2018 Methods  
In this chapter, we outline the development of the RNA-As-Graphs (or RAG) approach and highlight current applications to RNA structure prediction and design.  ...  The structure of RNA has been a natural subject for mathematical modeling, inviting many innovative computational frameworks.  ...  The author is grateful to Swati Jain for preparing many of the figures. Literature cited  ... 
doi:10.1016/j.ymeth.2018.03.009 pmid:29621619 pmcid:PMC6051918 fatcat:bfsktwmieve4ro7sys6ehc3pfa

RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology

Namhee Kim, Zhe Zheng, Shereef Elmetwaly, Tamar Schlick, Kay Hamacher
2014 PLoS ONE  
To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general.  ...  Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks.  ...  Naoto Baba for providing graph data for 11 vertices. We also thank Dr. Louis Petingi for his suggestions and general comments on networks, including partitioning.  ... 
doi:10.1371/journal.pone.0106074 pmid:25188578 pmcid:PMC4154854 fatcat:hj2whpdixrdpvhzacj6blhtf4a

A pipeline for computational design of novel RNA-like topologies

Swati Jain, Alain Laederach, Silvia B V. Ramos, Tamar Schlick
2018 Nucleic Acids Research  
Following partitioning of the target graph, corresponding atomic fragments from our RAG-3D database are combined using F-RAG, and the candidate atomic models are scored using a knowledge-based potential  ...  We describe a computational pipeline for design of novel RNA topologies based on our coarse-grained RNA-As-Graphs (RAG) framework.  ...  Bayrak, Dr Gavin Bascom and Dr Ognjen Perišić for helpful discussions and comments, Charlotte Davison and Maggie Pan for their work as part of the Girls' Science, Technology, Engineering and Mathematics  ... 
doi:10.1093/nar/gky524 pmid:30137633 pmcid:PMC6101589 fatcat:t5tacyqkoragjcrbfbksoy33nm

Opportunities and Challenges in RNA Structural Modeling and Design

Tamar Schlick, Anna Marie Pyle
2017 Biophysical Journal  
Churchill Simplified graph representations of RNA secondary structures that provide good candidate predictions of global RNA scaffold and present RNA design targets require automatic generation of atomic  ...  Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used  ...  We are grateful for partial support of the workshop by the National Institute of General Medical Sciences (NIGMS) award No.  ... 
doi:10.1016/j.bpj.2016.12.037 pmid:28162235 pmcid:PMC5529161 fatcat:i55b65jtybhfrhxnskde3umbvm

Frequent subgraph mining for biologically meaningful structural motifs [article]

Sebastian Keller, Pauli Miettinen, Olga V. Kalinina
2020 bioRxiv   pre-print
Finally we use the approach to discover a novel structural motif in jelly-roll capsid proteins found in members of the picornavirus-like superfamily.  ...  Here we present a novel approach to identify such motifs in protein three-dimensional structures without depending on sequence alignment by representing structures as graphs in the form of residue interaction  ...  Graph-based representations of protein three-dimensional structures Approaches that, like our approach, use graph representations of the protein 3D structures are a subset of the methods for finding structural  ... 
doi:10.1101/2020.05.14.095695 fatcat:3bfahgozlvcivg4xwacjox2jg4

Network Theory Tools for RNA Modeling

Namhee Kim, Louis Petingi, Tamar Schlick
2013 WSEAS Transactions on Mathematics  
By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies.  ...  An introduction into the usage of graph or network theory tools for the study of RNA molecules is presented.  ...  Acknowledgements: This work is supported by the National Science Foundation (DMS-0201160, CCF-0727001) and the National Institutes of Health (GM081410, GM100469).  ... 
pmid:25414570 pmcid:PMC4235620 fatcat:olt7kbyxu5frpfunqs6vjrbzoy

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs

Swati Jain, Cigdem Bayrak, Louis Petingi, Tamar Schlick
2018 Genes  
For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking  ...  We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges.  ...  Loren Williams for motivating the rRNA analysis and for providing initial data for rRNA structures. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes9080371 pmid:30044451 fatcat:lgy22h2vtfcqpdph7tb2qbhkhm

Predicting Helical Topologies in RNA Junctions as Tree Graphs

Christian Laing, Segun Jung, Namhee Kim, Shereef Elmetwaly, Mai Zahran, Tamar Schlick, Rafael Josef Najmanovich
2013 PLoS ONE  
First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with  ...  The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical  ...  Acknowledgements Molecular images were generated using the VMD program [57] . Author Contributions  ... 
doi:10.1371/journal.pone.0071947 pmid:23991010 pmcid:PMC3753280 fatcat:slqfm6imrraq3oifsw5kzbfdiu

Feature-Based Visual Analytics for Studying Simulations of Dynamic Bi-Stable Spatial Systems [article]

C. Eichner, A. Bittig, H. Schumann, C. Tominski
2013 International EuroVis Workshop on Visual Analytics  
With the help of the feature-based approach the scientists were able to understand how the spatial separation of proteins develops over time.  ...  representation of features with their spatial, temporal, and structural aspects.  ...  We visualize the feature graph (1) in a dedicated view that focuses on temporal aspects and (2) as a novel fusion of spatial, temporal and structural aspects.  ... 
doi:10.2312/pe.eurovast.eurova13.025-029 dblp:conf/eurova-ws/EichnerBST13 fatcat:uydxslhiq5hpfdnbfea6qtujey

APPLICATION OF SUPPORT VECTOR MACHINES IN VIRTUAL SCREENING

Soumi Sengupta, Sanghamitra Bandyopadhyay
2012 International Journal for Computational Biology  
The features generated in this way have been further used by the novel graph alignment kernel function to build SVM models for virtual screening.  ...  This approach is more useful when the structural information of the target protein in unknown.  ... 
doi:10.34040/ijcb.1.1.2012.20 fatcat:rqehr3xitfg43b3tfrgxufrmse

Recognition of Binding Patterns Common to a Set of Protein Structures [chapter]

Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson
2005 Lecture Notes in Computer Science  
We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures.  ...  We discuss the theoretical aspects of the computational problem of multiple structure alignment. This problem involves solving a 3D kpartite matching problem, which we show to be NP-Hard.  ...  A matching of a K- partite-3D graph is a set of disjoint K-tuples {(p t1 , ..., p t K ) : p ti ∈ S i , p tj ∈ S j , (p ti , p tj ) ∈ E}. Definition 5. (K-partite-3D-pivot graph).  ... 
doi:10.1007/11415770_33 fatcat:tosd5tf5r5bjplfdnwxjwu6aoa

Maximum Cliques in Protein Structure Comparison [chapter]

Noël Malod-Dognin, Rumen Andonov, Nicola Yanev
2010 Lecture Notes in Computer Science  
Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite graphs, referred here as alignment graphs.  ...  In this paper, we propose a new protein structure comparison method based on internal distances (DAST) which is posed as a maximum clique problem in an alignment graph.  ...  We would like to express our gratitude to J-F Gibrat for numerous helpful discussions and for providing us the source code of VAST.  ... 
doi:10.1007/978-3-642-13193-6_10 fatcat:u4akllxcuzcbrekp6mf5ropsi4

Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections

Eric J. Verbeke, Yi Zhou, Andrew P. Horton, Anna L. Mallam, David W. Taylor, Edward M. Marcotte
2019 Journal of Structural Biology  
We then apply our algorithm on cryo-EM data collected from a mixture of five protein complexes and use existing methods to solve multiple three-dimensional structures ab initio.  ...  The feasibility of this approach is first demonstrated on a large set of synthetic reprojections from 35 unique macromolecular structures spanning a mass range of hundreds to thousands of kilodaltons.  ...  Musalgaonkar and A. Johnson for providing 40S and 60S yeast ribosomes; A. Dai for expert cryo-EM assistance at the Sauer Structural Biology Laboratory at UT Austin; and members of the Taylor  ... 
doi:10.1016/j.jsb.2019.107416 pmid:31726096 pmcid:PMC6952565 fatcat:spg2sfvoxnb4nekr4dkdleve7e

Identifying Structural Domains in Proteins [chapter]

Lorenz Wernisch, Shoshana J. Wodak
2005 Methods of biochemical analysis  
The procedure implemented in STRUDL views the protein as a 3D graph of interacting residues, with no reference to any covalent structure.  ...  However, this approach is not limited to proteins with solved 3D structures.  ... 
doi:10.1002/0471721204.ch18 fatcat:lpsoifn3ffbqth6laf4ihw7juq
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