Property prediction by similarity of molecular structures—practical application and consistency analysis

2005 ◽  
Vol 60 (20) ◽  
pp. 5458-5471 ◽  
Author(s):  
Neima Brauner ◽  
Mordechai Shacham ◽  
Georgi St. Cholakov ◽  
Roumiana P. Stateva
Keyword(s):  
Molecular Structures ◽  
Practical Application ◽  
Consistency Analysis ◽  
Property Prediction

Property prediction by correlations based on similarity of molecular structures

AIChE Journal ◽  
2004 ◽  
Vol 50 (10) ◽  
pp. 2481-2492 ◽  
Author(s):  
Mordechai Shacham ◽  
Neima Brauner ◽  
Georgi Cholakov ◽  
Roumiana P. Stateva
Keyword(s):  
Molecular Structures ◽  
Property Prediction

scholarly journals Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields

2020 ◽  
Author(s):  
Victoria T. Lim ◽  
David F. Hahn ◽  
Gary Tresadern ◽  
Christopher I. Bayly ◽  
David Mobley
Keyword(s):  
Force Field ◽  
Small Molecules ◽  
Force Fields ◽  
Molecular Structures ◽  
Property Prediction ◽  
Benchmark Assessment ◽  
Heavy Atoms ◽  
Comparable Level ◽  
Optimized Geometries

<div>Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. </div><div>Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1 and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared these to reference quantum mechanical (QM) data. We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94s and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Our molecule set and results are available for other researchers to use in testing.</div>

Applied Research on Prediction Methods of Properties of Particleboard Based on Data-Driven Methods

2021 ◽  
Vol 15 (1) ◽  
pp. 1-9
Author(s):  
Cuiping Yang ◽  
Weiwen Lai ◽  
Jilai Su ◽  
Wei He ◽  
Zhenhua Gao
Keyword(s):  
Applied Research ◽  
Physical And Mechanical Properties ◽  
Decisive Role ◽  
Data Driven ◽  
Prediction Methods ◽  
Practical Application ◽  
Data Set ◽  
Property Prediction ◽  
Random Forest Method ◽  
Destructive Methods

As a kind of wood-based panel, particleboard is widely used in production and daily life. The physical and mechanical properties (PMPs) of particleboard play a decisive role in its practical application. At present, destructive methods are primarily used to measure the actual properties of particleboard on the production line, which is a waste of resources and time-consuming method. In order to solve these problems, this paper uses several data-driven methods to predict the PMPs of particleboard. Firstly, the data set is constructed based on the parameters of particleboard production process. Secondly, seven commonly used data-driven methods are used to build models to predict the PMPs. Finally, three different assessment indexes are used to determine the most suitable method for property prediction. The results showed that the random forest method is better for predicting the PMPs of particleboard.

Property prediction and consistency analysis by a reference series method

AIChE Journal ◽  
2012 ◽  
Vol 59 (2) ◽  
pp. 420-428 ◽  
Author(s):  
Mordechai Shacham ◽  
Inga Paster ◽  
Neima Brauner
Keyword(s):  
Series Method ◽  
Reference Series ◽  
Consistency Analysis ◽  
Property Prediction

scholarly journals Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields

2020 ◽  
Author(s):  
Victoria T. Lim ◽  
David F. Hahn ◽  
Gary Tresadern ◽  
Christopher I. Bayly ◽  
David Mobley
Keyword(s):  
Force Field ◽  
Small Molecules ◽  
Force Fields ◽  
Molecular Structures ◽  
Property Prediction ◽  
Benchmark Assessment ◽  
Heavy Atoms ◽  
Comparable Level ◽  
Optimized Geometries

<div>Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. </div><div>Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1 and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared these to reference quantum mechanical (QM) data. We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94s and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Our molecule set and results are available for other researchers to use in testing.</div>

Electron Microscopy in Molecular Biology

1967 ◽  
Vol 25 ◽  
pp. 2-3
Author(s):  
Cecil E. Hall
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Noise Level ◽  
Molecular Structures ◽  
Material Structure ◽  
The Arts ◽  
Shadow Casting ◽  
Electron Image ◽  
High Degree ◽  
Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

Progress In The Practical Application Of Automated Image Analysis To Tem Negatives

1977 ◽  
Vol 35 ◽  
pp. 214-217
Author(s):  
F. A. Heckman ◽  
E. Redman ◽  
J.E. Connolly
Keyword(s):  
Image Analysis ◽  
Image Quality ◽  
Exposure Time ◽  
Image Contrast ◽  
Automated Image Analysis ◽  
Practical Application ◽  
Factors Affecting ◽  
High Image Quality ◽  
Qualitative Evidence ◽  
Comprehensive Study

In our initial publication on this subject1) we reported results demonstrating that contrast is the most important factor in producing the high image quality required for reliable image analysis. We also listed the factors which enhance contrast in order of the experimentally determined magnitude of their effect. The two most powerful factors affecting image contrast attainable with sheet film are beam intensity and KV. At that time we had only qualitative evidence for the ranking of enhancing factors. Later we carried out the densitometric measurements which led to the results outlined below.Meaningful evaluations of the cause-effect relationships among the considerable number of variables in preparing EM negatives depend on doing things in a systematic way, varying only one parameter at a time. Unless otherwise noted, we adhered to the following procedure evolved during our comprehensive study:Philips EM-300; 30μ objective aperature; magnification 7000- 12000X, exposure time 1 second, anti-contamination device operating.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

Molecular architecture and functions of the neuronal cytoskeleton

1990 ◽  
Vol 48 (3) ◽  
pp. 2-3
Author(s):  
Nobutaka Hirokawa
Keyword(s):  
Major Elements ◽  
Molecular Structures ◽  
Organelle Transport ◽  
Molecular Architecture ◽  
Neuronal Morphogenesis ◽  
Microtubule Associated Proteins ◽  
Associated Proteins ◽  
And Function ◽  
Small Clusters

In this symposium I will present our studies about the molecular architecture and function of the cytomatrix of the nerve cells. The nerve cell is a highly polarized cell composed of highly branched dendrites, cell body, and a single long axon along the direction of the impulse propagation. Each part of the neuron takes characteristic shapes for which the cytoskeleton provides the framework. The neuronal cytoskeletons play important roles on neuronal morphogenesis, organelle transport and the synaptic transmission. In the axon neurofilaments (NF) form dense arrays, while microtubules (MT) are arranged as small clusters among the NFs. On the other hand, MTs are distributed uniformly, whereas NFs tend to run solitarily or form small fascicles in the dendrites Quick freeze deep etch electron microscopy revealed various kinds of strands among MTs, NFs and membranous organelles (MO). These structures form major elements of the cytomatrix in the neuron. To investigate molecular nature and function of these filaments first we studied molecular structures of microtubule associated proteins (MAP1A, MAP1B, MAP2, MAP2C and tau), and microtubules reconstituted from MAPs and tubulin in vitro. These MAPs were all fibrous molecules with different length and formed arm like projections from the microtubule surface.

Fifth Edition: the New Standard

2000 ◽  
Vol 5 (6) ◽  
pp. 1-7
Author(s):  
Christopher R. Brigham ◽  
James B. Talmage ◽  
Leon H. Ensalada
Keyword(s):  
Musculoskeletal System ◽  
Medical Information ◽  
Objective Assessment ◽  
Scientific Data ◽  
Practical Application ◽  
Fourth Edition ◽  
Appropriate Use ◽  
Medical Evaluation ◽  
Single Set

Abstract The AMA Guides to the Evaluation of Permanent Impairment (AMA Guides), Fifth Edition, is available and includes numerous changes that will affect both evaluators who and systems that use the AMA Guides. The Fifth Edition is nearly twice the size of its predecessor (613 pages vs 339 pages) and contains three additional chapters (the musculoskeletal system now is split into three chapters and the cardiovascular system into two). Table 1 shows how chapters in the Fifth Edition were reorganized from the Fourth Edition. In addition, each of the chapters is presented in a consistent format, as shown in Table 2. This article and subsequent issues of The Guides Newsletter will examine these changes, and the present discussion focuses on major revisions, particularly those in the first two chapters. (See Table 3 for a summary of the revisions to the musculoskeletal and pain chapters.) Chapter 1, Philosophy, Purpose, and Appropriate Use of the AMA Guides, emphasizes objective assessment necessitating a medical evaluation. Most impairment percentages in the Fifth Edition are unchanged from the Fourth because the majority of ratings currently are accepted, there is limited scientific data to support changes, and ratings should not be changed arbitrarily. Chapter 2, Practical Application of the AMA Guides, describes how to use the AMA Guides for consistent and reliable acquisition, analysis, communication, and utilization of medical information through a single set of standards.

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