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Shape Complementarity Analysis for Objects of Arbitrary Shape [article]

Morad Behandish, Horea T. Ilies
2017 arXiv   pre-print
However, the current challenge lies in the lack of a general mathematical formulation that applies to objects of arbitrary shape.  ...  The basic problem of shape complementarity analysis appears fundamental to applications as diverse as mechanical design, assembly automation, robot motion planning, micro- and nano-fabrication, protein-ligand  ...  However, in spite of its ubiquity and versatility, obtaining a general measure of shape complementarity for objects of arbitrary shape remains an open problem.  ... 
arXiv:1712.00238v1 fatcat:hhbaslwnyfaxfbcfpgng6k6vje

Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures

J. M. Friedman
1997 Protein Engineering Design & Selection  
We describe an improved method for determining the shapes and positions of ligand binding sites on proteins by calculating difference contact surfaces of proteins.  ...  This method for determining the shape and location of substrate binding sites has successfully located a number of experimentally observed substrate binding sites for several different ligands bound to  ...  We also thank Zbyszek Otwinowski (Yale University and University of Texas Southwestern Medical Center at Dallas) and B.Montgomery Pettitt (University of Houston) for useful suggestions and for use of computer  ... 
doi:10.1093/protein/10.8.851 pmid:9415436 fatcat:whjw3fc22nhr3ljmsjazxgilnq

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.  ...  To this end, moment-based representations provide a compact and nonredundant description of molecular shape and other associated properties.  ...  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

Page 1001 of Psychological Abstracts Vol. 82, Issue 3 [page]

1995 Psychological Abstracts  
Action, Paris, France) The visual of three-dimensional shape from self-motion and object-motion. Vision Research, 1994(Sep), Vol 34(18), 2331-2336.  ...  - lation (ST), object-translation (OT), or rotation of the object in depth (OR).  ... 

Co-generation of Collision-Free Shapes for Arbitrary One-Parametric Motion [article]

Clinton B. Morris, Morad Behandish
2022 arXiv   pre-print
For example, for a pair of parts undergoing a given relative motion, to make the problem well-posed, the geometry of one part (chosen arbitrarily) must be fixed to compute the maximal shape of the other  ...  In this paper, we formalize this family of collision-free shapes and introduce a generic method for generating a broad subset of them.  ...  Acknowledgments The authors are thankful to Amir Mirzendehdel for his insights on topology optimization and Saigopal Nelaturi for his support of this project under the Design for Assembly research program  ... 
arXiv:2205.05760v2 fatcat:vyhflkpgqbeetgoijwxptznbp4

SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity

A. Axenopoulos, P. Daras, G. E. Papadopoulos, E. N. Houstis
2013 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, a framework for protein-protein docking is proposed, which exploits both shape and physicochemical complementarity to generate improved docking predictions.  ...  Shape complementarity is achieved by matching local surface patches.  ...  Shape Impact Descriptor (SID) SID was firstly introduced in [15] and extended in [39] as a shape similarity measure for 3D objects.  ... 
doi:10.1109/tcbb.2012.149 pmid:23702550 fatcat:mee56lwzpbdhbovtuwx34trfhy

2D Zernike polynomial expansion: finding the protein-protein binding regions

Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, Giancarlo Ruocco
2020 Computational and Structural Biotechnology Journal  
Our method is able to rapidly and quantitatively measure the geometrical shape complementarity between interacting proteins, comparing their molecular iso-electron density surfaces expanding the surface  ...  We then apply the method for the blind recognition of binding sites, identifying the real region of interaction in about 60 % of the analyzed cases.  ...  describe the shape of each patch and rapidly assess its complementarity with others.  ... 
doi:10.1016/j.csbj.2020.11.051 pmid:33363707 pmcid:PMC7750141 fatcat:5raw5xzlvzgxrb4gpjoig7jcke

Docking Unbound Proteins with MIAX

Carlos A. Del Carpio Munoz, Tobias Peissker, Atsushi Yoshimori, Eiichiro Ichiishi
2003 Genome Informatics Series  
The methodology assists in deletion of atomic-scale details on the surface of the interacting monomers, leading to the extraction of the most characteristic flattened shape for the molecule as well as  ...  The methodology is characterized by its simplicity and easiness of embedment in any rigid body docking process based on point complementarity.  ...  Acknowledgments The present study was performed under the auspices of the Grant-in-Aid for Scientific Research on Priority Areas "Genome Information Science" No. 14015214 and 15014215 from the Ministry  ... 
doi:10.11234/gi1990.14.238 fatcat:h67dmne62vcsnookw2b3sdvzc4

Remembering Yasuto Mushiake [In Memoriam]

Qiang Chen, Kunio Sawaya, W. Ross Stone
2020 IEEE Antennas & Propagation Magazine  
Mushiake also applied Babinet's principle to the analysis of a slot antenna having an arbitrary shape.  ...  The importance of the radii of the wires was also applied to the analysis of V-shaped dipole antennas and crossed dipole antennas. The step-up impedance ratio of a folded dipole reported by Prof.  ... 
doi:10.1109/map.2020.3034504 fatcat:jzu5px733rdnlevsjy5cei37wm

Mathematical Tools of Soft Computing

Ker-Wei Yu, Yang Xu, Jer-Guang Hsieh
2014 Mathematical Problems in Engineering  
The nonlinear complementarity problem is investigated in the paper "An improved filter method for nonlinear complementarity problem" by K. Su et al.  ...  In the paper "Optimization and soft constraints for human shape and pose estimation based on a 3D morphable model" by D.  ...  Acknowledgments We wish to express our sincere appreciation to the authors for their excellent contributions. The hard work of all reviewers is greatly acknowledged.  ... 
doi:10.1155/2014/904014 fatcat:gs4ugjintbf5xopjwjq34tx5sq

Dense shape reconstruction of a moving object under arbitrary, unknown lighting

Simakov, Frolova, Basri
2003 Proceedings Ninth IEEE International Conference on Computer Vision  
We present a method for shape reconstruction from several images of a moving object. The reconstruction is dense (up to image resolution).  ...  The object is assumed Lambertian (completely matte), light sources should not be very close to the object but otherwise arbitrary, and no knowledge of lighting conditions is required.  ...  Conclusion We presented a method for shape reconstruction of a non-stationary object under arbitrary lighting.  ... 
doi:10.1109/iccv.2003.1238628 dblp:conf/iccv/SimakovFB03 fatcat:roibv5qjnzb7zdjd2qwbk4a2vu

Conformon-driven biopolymer shape changes in cell modeling

Sungchul Ji, Gabriel Ciobanu
2003 Biosystems (Amsterdam. Print)  
Given a set of space-and time-organized teleonomic shape changes of biopolymers driven by conformons, all of the functions of the cell can be accounted for in molecular terms-at least in principle.  ...  Conformons, defined as sequence-specific mechanical strains of biopolymers first invoked three decades ago to account for energy coupling in mitochondria, have been identified as shape changers, the agents  ...  He is also grateful for the generous financial support provided by the Mathematical Institute of the National University of Singapore, which allowed him to travel to Singapore to present two papers at  ... 
doi:10.1016/s0303-2647(03)00038-8 pmid:12915273 fatcat:oyo7eseimjf3hbvgh2n6ktbqea

Packing, entropic patchiness, and self-assembly of non-convex colloidal particles: A simulation perspective

Carlos Avendaño, Fernando A. Escobedo
2017 Current Opinion in Colloid & Interface Science  
The availability of such building blocks has motivated many computational studies on the formation of new materials driven by such complex effects as interpenetration, interlocking, and shape complementarity  ...  Recent advances in experimental techniques to synthesise particles with non-convex shapes have provided new challenges and opportunities to the modelling community.  ...  We are also familiar with classical shape sorting toys used to help toddlers to develop spatial skills in which particular geometrical objects can only fit in specific cavities (shape complementarity).  ... 
doi:10.1016/j.cocis.2017.05.005 fatcat:ley3ma7qcjcajgh6xanufurskm

The Geometry of Shape Space: Application to Influenza

ALAN LAPEDES, ROBERT FARBER
2001 Journal of Theoretical Biology  
The dimension of shape space deduced from hemagglutination inhibition assays for in#uenza is low, approximately "ve dimensional.  ...  The analysis techniques presented here are not restricted to the analysis of antibody}antigen interactions and are generally applicable to a$nity data resulting from binding assays.  ...  The authors thank Nancy Cox and members of the In#uenza Branch, Centers for Disease Control and Prevention, for generous provision of hemagglutination inhibition assay data for in#uenza and for useful  ... 
doi:10.1006/jtbi.2001.2347 pmid:11527445 fatcat:zsk77eh5yzcetie6jj3gfrpyqq

PECULIARITIES IN THE DIELECTRIC RESPONSE OF NEGATIVE-PERMITTIVITY SCATTERERS

Ari Henrik Sihvola
2006 Electromagnetic Waves  
A singular behavior between the limits of invisibility and infinite response is underlined for a hollow circular shell.  ...  The complementary principle for two-dimensional scatterers is used to derive special properties of self-complementary inclusions.  ...  a complete cloaking of arbitrary objects by tracing and dragging wave rays past it [9] [10] [11] [12] .  ... 
doi:10.2528/pier06112001 fatcat:mw2mecce5vc2fn63nyd6iws224
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