ALCHEMY III, Three-Dimensional Molecular Modeling Software

1992 ◽  
Vol 32 (6) ◽  
pp. 753-754
Author(s):  
William Gleason ◽  
William Ojala
Keyword(s):  
Molecular Modeling ◽  
Three Dimensional ◽  
Modeling Software

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals An Anatomically Placed Tibial Tunnel does not Completely Surround a Simulated PCL Reconstruction Graft in the Proximal Tibia

2022 ◽  
Author(s):  
Christopher Kim ◽  
Dustin Baker ◽  
Brian Albers ◽  
Scott G. Kaar
Keyword(s):  
Surface Area ◽  
Cruciate Ligament ◽  
Tibial Tunnel ◽  
Three Dimensional ◽  
Pcl Reconstruction ◽  
Posterior Cortex ◽  
Modeling Software ◽  
The Mean ◽  
Tibial Cortex ◽  
Area And Volume

Abstract Introduction It is hypothesized that anatomic tunnel placement will create tunnels with violation of the posterior cortex and subsequently an oblique aperture that is not circumferentially surrounded by bone. In this article, we aimed to characterize posterior cruciate ligament (PCL) tibial tunnel using a three-dimensional (3D) computed tomography (CT) model. Methods Ten normal knee CTs with the patella, femur, and fibula removed were used. Simulated 11 mm PCL tibial tunnels were created at 55, 50, 45, and 40 degrees. The morphology of the posterior proximal tibial exit was examined with 3D modeling software. The length of tunnel not circumferentially covered (cortex violation) was measured to where the tibial tunnel became circumferential. The surface area and volume of the cylinder both in contact with the tibial bone and that not in contact with the tibia were determined. The percentages of the stick-out length surface area and volume not in contact with bone were calculated. Results The mean stick-out length of uncovered graft at 55, 50, 45, and 40 degrees were 26.3, 20.5, 17.3, and 12.7 mm, respectively. The mean volume of exposed graft at 55, 50, 45, and 40 degrees were 840.8, 596.2, 425.6, and 302.9 mm3, respectively. The mean percent of volume of exposed graft at 55, 50, 45, and 40 degrees were 32, 29, 25, and 24%, respectively. The mean surface of exposed graft at 55, 50, 45, and 40 degrees were 372.2, 280.4, 208.8, and 153.3 mm2, respectively. The mean percent of surface area of exposed graft at 55, 50, 45, and 40 degrees were 40, 39, 34, and 34%, respectively. Conclusion Anatomic tibial tunnel creation using standard transtibial PCL reconstruction techniques consistently risks posterior tibial cortex violation and creation of an oblique aperture posteriorly. This risk is decreased with decreasing the angle of the tibial tunnel, though the posterior cortex is still compromised with angles as low as 40 degrees. With posterior cortex violation, a surgeon should be aware that a graft within the tunnel or socket posteriorly may not be fully in contact with bone. This is especially relevant with inlay and socket techniques.

scholarly journals Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

2019 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Geoffrey Hutchison
Keyword(s):  
Molecular Modeling ◽  
Structure Prediction ◽  
Distance Geometry ◽  
Three Dimensional ◽  
Property Prediction ◽  
Crystallographic Databases ◽  
Fragment Library ◽  
Wide Range ◽  
Computational Property ◽  
Improving Accuracy

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

3D Printed Glitches

2019 ◽  
pp. 70-93
Author(s):  
James F. Kerestes
Keyword(s):  
Higher Education ◽  
3D Printing ◽  
Three Dimensional ◽  
The United States ◽  
Three Dimensional Modeling ◽  
Modeling Software ◽  
Common Resource ◽  
Education Design ◽  
3D Printed ◽  
Architecture And Design

3D printing is a common resource within the architecture and design disciplines in higher education. As is the case with all tools, there is a predetermined functionality and expected outcome when using additive manufacturing technology. There are also learning opportunities rooted in unforeseen equipment errors. The following chapter outlines alternate approaches for the use of 3D printing beyond mere representation and utilization in higher education design environments. Manufactured glitches enable students to analyze the predetermined functionality of the tools they engage with, and enter into a dialogue with technology as a medium for exploration and authorial exchange. To explore these concepts, a series of case studies that tested the parameters of glitches in both digital (three-dimensional modeling software) and physical mediums (rapid prototyping) was completed by a group of architecture and design students at a Midwestern University in the United States.

scholarly journals Manufacturing of Flexible Surgical Guide for Fully Edentulous Patients

2012 ◽  
Vol 488-489 ◽  
pp. 1001-1005 ◽  
Author(s):  
Jamal Kashani ◽  
Zohreh Arabshahi ◽  
Mohammed Rafiq Abdul Kadir ◽  
Abbas Azari
Keyword(s):  
Three Dimensional ◽  
Internal Diameter ◽  
Surgical Guide ◽  
Three Dimensional Modeling ◽  
Surgical Guides ◽  
Dimensional Modeling ◽  
Drill Diameter ◽  
Modeling Software ◽  
Three Dimensional Models ◽  
Edentulous Patients

Despite efficiency of modern implantology, unplanned perforation and drill deviation could be happened during freehand placement. The aim of this study was to provide a methodology for fabricating dental surgical drill guide for fully edentulous patients while it was flexible in term of changing drill diameter. The data of patient consisted of bone anatomy and radio-opaque template obtained from computed tomography. Jawbone and radio-opaque template three dimensional models converted into a three dimensional modeling software by means of an image processing package. Based on jawbone anatomy and radio-opaque template, implantation plan and design of surgical guides were carried out in three dimensional software. Rapid prototyping technique was used to manufacture several surgical guides to be used in different drilling sequences. Finally stainless steel tubes were accommodated passage of drill. Sequential surgical guides were different only in terms of the metal tubes internal diameter. This provides the ability of changing diameter of the implant or drill after fabricating surgical guide.

Research on the Application of Cellular Algorithm in 3D Modeling of Cartoon Characters

2014 ◽  
Vol 513-517 ◽  
pp. 1744-1747
Author(s):  
Feng Liu
Keyword(s):  
Design Method ◽  
Three Dimensional ◽  
Production Costs ◽  
3D Animation ◽  
Design Concepts ◽  
Three Dimensional Modeling ◽  
Modeling Software ◽  
High Production ◽  
Cartoon Characters ◽  
Time And Energy

The traditional design method of 3D animation modelings, by which can obtain attractive and precise 3D animation modelings, is to use three-dimensional modeling software such as Maya or 3D Max to draw directly. However, this method is faced with many problems, for instance, the lack of creativity, long design circle, high production costs, etc. For the problem of the lack of creativity, the reason is that animation designers are often subject to the limitation of the existing modelings and design concepts in the design process, therefore, they can not design creative modelings which are attractive and unforgettable enough. [For the problem of long design circle and high production costs, the reason is that although the 3D animation software are powerful, to skillfully master them not only requires users to have knowledge of computer technology and aesthetics at the same time, but also need a long learning process of modeling. Moreover, it takes the designers a lot of time and energy to design, draw and complete each modeling, and this will undoubtedly extend the design circle and increase the costs to some extent. Therefore, how to quickly and automatically generate creative 3D animation modelings has become a research focus of the present computer-aided creative design.

scholarly journals Three-Dimensional Molecular Modeling of Bovine Caseins

1994 ◽  
pp. 392-419
Author(s):  
Harold M. Farrell ◽  
Thomas F. Kumosinski ◽  
Gregory King
Keyword(s):  
Molecular Modeling ◽  
Three Dimensional
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