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3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison

Yu-Shen Liu, Meng Wang, Jean-Claude Paul, Karthik Ramani
2012 BMC Bioinformatics  
lead to incorrect measure of the shape similarity of flexible molecules.  ...  Compared to other shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules.  ...  Acknowledgements The MolMovDB database is provided by S Flores and M Gerstein.  ... 
doi:10.1186/1471-2105-13-95 pmid:22583488 pmcid:PMC3430558 fatcat:uax5z67yzvalfojtlzynl67usu

IDSS: deformation invariant signatures for molecular shape comparison

Yu-Shen Liu, Yi Fang, Karthik Ramani
2009 BMC Bioinformatics  
may lead to incorrect measure of the shape similarity of flexible molecules.  ...  Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC) treat them as rigid bodies, which  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Institutes of Health.  ... 
doi:10.1186/1471-2105-10-157 pmid:19463181 pmcid:PMC2694795 fatcat:u4x45t3r75ha3gd3xsxpene3xe

Three dimensional shape comparison of flexible proteins using the local-diameter descriptor

Yi Fang, Yu-Shen Liu, Karthik Ramani
2009 BMC Structural Biology  
The proposed method will be potentially useful for molecule retrieval with similar shapes and rapid structure retrieval for proteins.  ...  Results: We introduce an efficient approach for comparing flexible protein shapes by adapting a local diameter (LD) descriptor.  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Institute of Health.  ... 
doi:10.1186/1472-6807-9-29 pmid:19435524 pmcid:PMC2685140 fatcat:2ukg6qxpuvgd7jdnhcdwmtpzjm

Using diffusion distances for flexible molecular shape comparison

Yu-Shen Liu, Qi Li, Guo-Qin Zheng, Karthik Ramani, William Benjamin
2010 BMC Bioinformatics  
Results: In this paper, we present a new shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D shapes of flexible molecules.  ...  Conclusions: We illustrate that DDSD is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors.  ...  QL implemented the idea, and GZ participated in the research. KR identified the underlying opportunity and basis for connecting diffusion to shape analysis.  ... 
doi:10.1186/1471-2105-11-480 pmid:20868474 pmcid:PMC2949899 fatcat:3tbgklffsvfatdspi6plyc2uou

Novel technologies for virtual screening

Thomas Lengauer, Christian Lemmen, Matthias Rarey, Marc Zimmermann
2004 Drug Discovery Today  
Multiple FTree models capture local and global properties of the compounds and give statistics with only a minor loss of quality compared to the much more labor-and compute-intensive 3D comparative molecular  ...  Well-fitting fragments are combined to result in a molecule with high shape similarity to the given query.  ... 
doi:10.1016/s1359-6446(04)02939-3 pmid:14761803 fatcat:kigd5ydnirbphig6cv3ciyp4xy

Protein Binding Ligand Prediction Using Moments-Based Methods [chapter]

Rayan Chikhi, Lee Sael, Daisuke Kihara
2011 Protein Function Prediction for Omics Era  
A new development of pocket comparison method is also mentioned, which allows partial matching of pockets by using local patch descriptors.  ...  An advantage of moment-based methods is that the tertiary structure of pocket shapes is described compactly as a vector of coefficients of series expansion.  ...  Acknowledgements This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01 GM075004).  ... 
doi:10.1007/978-94-007-0881-5_8 fatcat:mqowzldesvfdzksjnmvzar4fam

Spatial chemical distance based on atomic property fields

A. V. Grigoryan, I. Kufareva, M. Totrov, R. A. Abagyan
2010 Journal of Computer-Aided Molecular Design  
Therefore, relying on chemical similarity to known binders in search for novel chemicals targeting the same protein artificially narrows down the results and makes lead hopping impossible.  ...  In fact for these cases we obtained improvement in 86% of domains compare to 2D Tanimoto measure and 85% compare to Shape Tanimoto measure.  ...  The second ligand was flexibly minimized in the obtained field in a search for the local minimum of its APF-score calculated as described above.  ... 
doi:10.1007/s10822-009-9316-x pmid:20229197 pmcid:PMC2858276 fatcat:nmudcs2gerch3ps6xwk453gtpy

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

Ashutosh Kumar, Kam Y. J. Zhang
2018 Frontiers in Chemistry  
A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules.  ...  In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets.  ...  Further, while these methods capture very well the global shape of a molecule, the local shape similarity is not represented comprehensively which is very critical in comparing the shapes of small molecules  ... 
doi:10.3389/fchem.2018.00315 pmid:30090808 pmcid:PMC6068280 fatcat:b2ieooqchfcepo7qe7u5cngtcy

Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery

Woong-Hee Shin, Xiaolei Zhu, Mark Bures, Daisuke Kihara
2015 Molecules  
Keywords Ligand-based virtual screening; Three-dimensional similarity; ROCS; USR; 3D Zernike descriptors; Patch-Surfer; PL-PatchSurfer; molecular shape; molecular surface licensee MDPI, Basel, Switzerland  ...  Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed.  ...  DK also acknowledges funding from the National Institute of General Medical Sciences of the National Institutes of Health (R01GM097528) and the National Science Foundation (IIS1319551, DBI1262189, IOS1127027  ... 
doi:10.3390/molecules200712841 pmid:26193243 pmcid:PMC5005041 fatcat:ajzknqtl3jewfmxammsgr6ylhy

Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map

Lee Sael, Daisuke Kihara
2010 International Journal of Knowledge Discovery in Bioinformatics  
We analyzed the similarity of local surface patches from 609 representative proteins considering shape and the electrostatic potential, which are represented by the 3D Zernike descriptors.  ...  Classification of local patches is done with the emergent self-organizing map (ESOM). We mapped patches at ligand bindingsites to investigate how they distribute and cluster among the ESOM map.  ...  Acknowledgment This work is supported by the the National Institutes of Health (GM075004 and GM077905) and National Science Foundation (DMS0604776, DMS800568). Local Protein Surface Classification 18  ... 
doi:10.4018/jkdb.2010100203 fatcat:zo5r3bxy7fahrbwsb3bnooov5e

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

Lee Sael, Daisuke Kihara
2012 Proteins: Structure, Function, and Bioinformatics  
Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets.  ...  The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function.  ...  This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM075004).  ... 
doi:10.1002/prot.24018 pmid:22275074 pmcid:PMC3294165 fatcat:x4dny7aqsbevjo62muy77cjxxu

Potential for Protein Surface Shape Analysis Using Spherical Harmonics and 3D Zernike Descriptors

Vishwesh Venkatraman, Lee Sael, Daisuke Kihara
2009 Cell Biochemistry and Biophysics  
We further discuss recent advances covering aspects of shape and property-based comparison at both global and local levels and demonstrate their applicability through some of our studies.  ...  In this article, we present an overview of some commonly used representations with specific focus on two schemes namely spherical harmonics and their extension, the 3D Zernike descriptors.  ...  Acknowledgments This work is supported by grants from the National Institutes of Health (R01 GM075004) and National Science Foundation (DMS0604776, DMS800568).  ... 
doi:10.1007/s12013-009-9051-x pmid:19521674 fatcat:b3a4dmdl5zdmvpkiswdzpdpv3i

Chemical Similarity Searching

Peter Willett, John M. Barnard, Geoffrey M. Downs
1998 Journal of chemical information and computer sciences  
New types of similarity measure are then compared with current approaches, and examples are given of several applications that are related to similarity searching.  ...  The next sections focus upon two of the principal characteristics of a similarity measure: the coefficient that is used to quantify the degree of structural resemblance between pairs of molecules and the  ...  The Krebs Institute for Biomolecular Research is a designated Biomolecular Sciences Centre of the Biotechnology and Biological Sciences Research Council.  ... 
doi:10.1021/ci9800211 fatcat:tdgj2n6c3jfzplxgpa4k7bs3zi

Fast Similarity Search in Three-Dimensional Structure Databases

Xiong Wang, Jason T. L. Wang
2000 Journal of chemical information and computer sciences  
Given a database D of three-dimensional (3D) molecular structures and a target molecule Q, the similarity search problem is to find the molecules O in D that match Q after allowing for an arbitrary number  ...  In this paper we study the similarity search problem and a class of related queries. We present a computer vision based technique, called geometric hashing, for processing these queries.  ...  Bruce Shapiro (National Cancer Institute), and Professor Dennis Shasha (New York University) for their inspirations and very helpful discussions during the preparation of the paper.  ... 
doi:10.1021/ci990081m pmid:10761151 fatcat:4wfqi3jmrrbpxfvyewu67ugvei

Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking

Daisuke Kihara, Lee Sael, Rayan Chikhi, Juan Esquivel-Rodriguez
2011 Current protein and peptide science  
We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces.  ...  To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions  ...  Acknowledgements This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM075004).  ... 
doi:10.2174/138920311796957612 pmid:21787306 fatcat:3nmgbp2dqfa65e74eb7bpx3hve
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