Nano-Kinematics for Analysis Of Protein Molecules

2004 ◽  
Vol 127 (4) ◽  
pp. 699-711 ◽  
Author(s):  
Kazem Kazerounian ◽  
Khalid Latif ◽  
Kimberly Rodriguez ◽  
Carlos Alvarado
Keyword(s):  
Software Package ◽  
Three Dimensional ◽  
Computer Software ◽  
Linear Structure ◽  
Data Bank ◽  
Kinematic Parameter ◽  
Rigid Bodies ◽  
Protein Chain ◽  
Kinematic Chains ◽  
Protein Molecules

Proteins are evolution’s mechanisms of choice. The study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. In this work, we have presented a comprehensive methodology for kinematics notation and direct kinematics for protein molecules. These methods utilize the zero-position analysis method and draws upon other recent advances in robot manipulation theories. The procedures involved in finding the coordinates of every atom in the protein chain as a function of the dihedral and Rotamer angles are computationally the most efficient formulation developed to date. The notation and the methodologies of this paper are incorporated in the computer software package PROTOFOLD and will be made available to individuals interested in using it. PROTOFOLD is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In addition to the new kinematics methodologies mentioned above, we have also included all the basic kinematic parameter values that are needed in any kinematic analysis involving proteins. While these values are based on a body of knowledge recorded in the protein data bank, they are presented in a form conducive to kinematics.

ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules

2004 ◽  
Author(s):  
Kazem Kazerounian ◽  
Khalid Latif ◽  
Kimberly Rodriguez ◽  
Carlos Alvarado
Keyword(s):  
Three Dimensional ◽  
Linear Structure ◽  
Rigid Bodies ◽  
Dynamics Simulation ◽  
Kinematic Chains ◽  
Simulation Techniques ◽  
Revolute Joints ◽  
Zero Position ◽  
Ab Initio Prediction ◽  
Protein Molecules

Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.

MIPS: metal interactions in protein structures

2009 ◽  
Vol 43 (1) ◽  
pp. 196-199 ◽  
Author(s):  
K. Hemavathi ◽  
M. Kalaivani ◽  
A. Udayakumar ◽  
G. Sowmiya ◽  
J. Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Metal Interactions ◽  
Structural Functions ◽  
Protein Molecules ◽  
Macromolecular Protein ◽  
And Function ◽  
Nucleic Acid Structures ◽  
User Friendly

MIPS (metal interactions in protein structures) is a database of metals in the three-dimensional macromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed database serves as an open resource for the analysis and visualization of all metals and their interactions with macromolecular (protein and nucleic acid) structures. MIPS can be searchedviaa user-friendly interface, and the interactions between metals and protein molecules, and the geometric parameters, can be viewed in both textual and graphical format using the freely available graphics plug-inJmol. MIPS is updated regularly, by means of programmed scripts to find metal-containing proteins from newly released protein structures. The database is useful for studying the properties of coordination between metals and protein molecules. It also helps to improve understanding of the relationship between macromolecular structure and function. This database is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, around the clock, at http://dicsoft2.physics.iisc.ernet.in/mips/.

Self-Collision Detection in Spatial Closed Chains

2008 ◽  
Vol 130 (9) ◽  
Author(s):  
John S. Ketchel ◽  
Pierre M. Larochelle
Keyword(s):  
Motion Planning ◽  
Finite Length ◽  
Collision Detection ◽  
Three Dimensional ◽  
Detection Algorithm ◽  
Rigid Bodies ◽  
Three Dimensions ◽  
Circular Cylinders ◽  
Infinite Length ◽  
Kinematic Chains

A novel methodology for detecting self-collisions in spatial closed kinematic chains is presented. In general these chains generate complex three dimensional motions in which their own links will collide with each other (i.e., a self-collision) without effective motion planning. The self-collision detection is accomplished via a novel algorithm for definitively detecting collisions of right circular, cylindrically shaped, rigid bodies moving in three dimensions. The algorithm uses line geometry and dual number algebra to exploit the geometry of right circular cylindrical objects to facilitate the detection of collisions. In the first stage of the algorithm, cylindrically shaped rigid bodies are modeled by infinite length right circular cylinders. Sufficient and necessary conditions are then used to determine if a pair of infinite length cylinders collide. If the actual finite length rigid bodies collide, then it is necessary that their associate infinite length cylinder models collide, and we proceed to the next stage of the algorithm where the bodies are modeled with finite length cylinders and a definitive necessary and sufficient collision detection algorithm is employed. The result is an efficient approach of detecting collisions of cylindrically shaped bodies moving in three dimensions that has applications in spatial mechanism design and motion planning. A case study examining a spatial 4C mechanism for self-collisions is included.

scholarly journals A computer-based approach for developing linamarase inhibitory agents

2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Lucas Paul ◽  
Celestin N. Mudogo ◽  
Kelvin M. Mtei ◽  
Revocatus L. Machunda ◽  
Fidele Ntie-Kang
Keyword(s):  
Structure Elucidation ◽  
Three Dimensional ◽  
Data Bank ◽  
Competitive Inhibitor ◽  
Industrial Applications ◽  
Dimensional Structure ◽  
Full Understanding ◽  
The Poor ◽  
Computer Based ◽  
Inhibitory Agents

AbstractCassava is a strategic crop, especially for developing countries. However, the presence of cyanogenic compounds in cassava products limits the proper nutrients utilization. Due to the poor availability of structure discovery and elucidation in the Protein Data Bank is limiting the full understanding of the enzyme, how to inhibit it and applications in different fields. There is a need to solve the three-dimensional structure (3-D) of linamarase from cassava. The structural elucidation will allow the development of a competitive inhibitor and various industrial applications of the enzyme. The goal of this review is to summarize and present the available 3-D modeling structure of linamarase enzyme using different computational strategies. This approach could help in determining the structure of linamarase and later guide the structure elucidation in silico and experimentally.

scholarly journals BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 180
Author(s):  
Zorana Lopandić ◽  
Luka Dragačević ◽  
Dragan Popović ◽  
Uros Andjelković ◽  
Rajna Minić ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Lectin Binding ◽  
Three Dimensional ◽  
Data Bank ◽  
Salmonella Typhi ◽  
Excitation Wavelength ◽  
Protein Data Bank Entry ◽  
High Mannose

Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.

scholarly journals Application of the erosion algorithm in modeling of structures behavior under impulse loads

2019 ◽  
Vol 221 ◽  
pp. 01003
Author(s):  
Pavel Radchenko ◽  
Stanislav Batuev ◽  
Andrey Radchenko
Keyword(s):  
Finite Element ◽  
High Velocity ◽  
Three Dimensional ◽  
Computer Software ◽  
Dynamic Loads ◽  
Complex Structures ◽  
Numerical Studies ◽  
Contact Surfaces ◽  
Fracture Of Materials ◽  
Solid Bodies

The paper presents results of applying approach to simulation of contact surfaces fracture under high velocity interaction of solid bodies. The algorithm of erosion -the algorithm of elements removing, of new surface building and of mass distribution after elements fracture at contact boundaries is consider. The results of coordinated experimental and numerical studies of fracture of materials under impact are given. Authors own finite element computer software program EFES, allowing to simulate a three-dimensional setting behavior of complex structures under dynamic loads, has been used for the calculations.

Design of a 6-DOF Robotic Gait Training System With Closed-Chain Foot Initiated Kinematics Control

2015 ◽  
Author(s):  
Wei Liu ◽  
John Kovaleski ◽  
Marcus Hollis
Keyword(s):  
Three Dimensional ◽  
Computer Software ◽  
Gait Training ◽  
Gait Pattern ◽  
Training System ◽  
Normal Walking ◽  
Robot Assisted ◽  
Walking Gait ◽  
The Right ◽  
Joint Motions

Robotic assisted rehabilitation, taking advantage of neuroplasticity, has been shown to be helpful in regaining some degree of gait performance. Robot-applied movement along with voluntary efferent motor commands coordinated with the robot allows optimization of motion training. We present the design and characteristics of a novel foot-based 6-degree-of-freedom (DOF) robot-assisted gait training system where the limb trajectory mirrored the normal walking gait. The goal of this study was to compare robot-assisted gait to normal walking gait, where the limb moved independently without robotics. Motion analysis was used to record the three-dimensional kinematics of the right lower extremity. Walking motion data were determined and transferred to the robotic motion application software for inclusion in the robotic trials where the robot computer software was programmed to produce a gait pattern in the foot equivalent to the gait pattern recorded from the normal walking gait trial. Results demonstrated that ankle; knee and hip joint motions produced by the robot are consistent with the joint motions in walking gait. We believe that this control algorithm provides a rationale for use in future rehabilitation, targeting robot-assisted training in people with neuromuscular disabilities such as stroke.

Issues on Teaching Kinematics and Mechanism Design

1992 ◽  
Author(s):  
Arthur G. Erdman ◽  
Thomas R. Corrigan
Keyword(s):  
Mechanism Design ◽  
Software Package ◽  
Computer Software ◽  
Computer Solution ◽  
Design Problems ◽  
Introductory Course ◽  
Modern Computer ◽  
Computer Software Package ◽  
Historical Examination

Abstract The issues, problems and possible solutions involved in teaching a modern course on mechanisms and kinematics are addressed from the perspective of a professor and a student. A historical examination shows the value of modern (computer) solution of classical dilemmas. The structure of an introductory course is then presented, with comments on its educational attributes. The solution of several design problems with LINCAGES©, a computer software package, demonstrates the prowess of the modem student/computer liaison.

EVALUATION OF POSSIBILITIES TO IMPROVE RIGID BODIES

2020 ◽  
Vol 69 (1) ◽  
pp. 392-395
Author(s):  
N.M. Nurullayev ◽  
◽  
D.A. Turgunboyev ◽  
Ye.N. Zholdassov ◽  
◽  
...  
Keyword(s):  
Literature Review ◽  
Software Package ◽  
Scientific Research ◽  
Rigid Bodies ◽  
Robotic Arm ◽  
Electromechanical Devices ◽  
End Effectors ◽  
External Characteristics

Manipulators are used for various purposes in order to simplify tasks or reduce the risk of tasks that are considered impossible, dangerous or difficult for humans. The robotic arm can be equipped with various types of end effectors to perform a variety of tasks. Grips are one of the most commonly used tools for manipulators. This article discusses the analysis of modeling new robotic gripping fingers, based on models of gripping gross rigid bodies of manipulators. A literature review was conducted in the relevant branches of scientific research. The ability to minimize dimensions and masses, as well as the final cost of the product, using available materials and electromechanical devices, various sensors, is evaluated. The external characteristics that make the previously developed analogues ineffective are analyzed. Modeling was released using the SolidWorks software package.

Effect of Material and Geometric Parameters on the Steady-State Belt Stresses and Belt Slip for Flat Belt-Drives

2015 ◽  
Author(s):  
Cagkan Yildiz ◽  
Tamer M. Wasfy ◽  
Hatem M. Wasfy ◽  
Jeanne M. Peters
Keyword(s):  
Steady State ◽  
Equations Of Motion ◽  
Three Dimensional ◽  
Flexible Multibody Dynamics ◽  
Friction Model ◽  
Rigid Bodies ◽  
Geometric Parameters ◽  
Rubber Matrix ◽  
Axial Stiffness ◽  
Belt Drive

In order to accurately predict the fatigue life and wear life of a belt, the various stresses that the belt is subjected to and the belt slip over the pulleys must be accurately calculated. In this paper, the effect of material and geometric parameters on the steady-state stresses (including normal, tangential and axial stresses), average belt slip for a flat belt, and belt-drive energy efficiency is studied using a high-fidelity flexible multibody dynamics model of the belt-drive. The belt’s rubber matrix is modeled using three-dimensional brick elements and the belt’s reinforcements are modeled using one dimensional truss elements. Friction between the belt and the pulleys is modeled using an asperity-based Coulomb friction model. The pulleys are modeled as cylindrical rigid bodies. The equations of motion are integrated using a time-accurate explicit solution procedure. The material parameters studied are the belt-pulley friction coefficient and the belt axial stiffness and damping. The geometric parameters studied are the belt thickness and the pulleys’ centers distance.

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