1. SHELX for Macromolecules - George M. Sheldrick
A new version of the complete SHELX system is being released in 1996. In addition to SHELXS-96 (structure solution) and SHELXL-96 (refinement) there are several auxiliary programs, including an interface program SHELXPRO for protein applications. Although SHELX was originally designed for small molecules, the new Patterson interpretation routine in SHELXS-96 is useful for the location of heavy atoms from DF data, and SHELXL-96 facilitates the refinement of macromolecules against high resolution data. 1 Introduction The first version of SHELX was written about 25 years ago. The gradual emergence of a relatively portable FORTRAN subset enabled it to be distributed (in compressed form including test data as one box of punched cards) in 1976. SHELX-76 survived...

2. Simple Models of Biological Macromolecules - E. G. Timoshenko
We present a brief overview of simple statistical mechanical models of biopolymers such as proteins and nucleic acids. These are studied by the Gaussian self--consistent method and direct Monte Carlo simulations. The equilibrium phase diagrams and kinetics of conformational transitions between different states are elucidated. Amphiphilic copolymers and the persistent homopolymer considered here exhibit a remarkable variety of conformational states with a rather complex multistage kinetics of folding from the extended coil into compact globular states. 1 Introduction Complexity and huge size of biological macromolecules [1] makes their modelling and analysis an exteremely hard if not an impossible task. The helix of DNA which is closed packed into...

3. Efficient Discovery of Common Substructures in Macromolecules - Srinivasan Parthasarathy,Matt Coatney
Biological macromolecules play a fundamental role in disease; therefore, they are of great interest to fields such as pharmacology and chemical genomics. Yet due to macromolecules ' complexity, development of effective techniques for elucidating structure-function macromolecular relationships has been ill explored. Previous techniques have either focused on sequence analysis, which only approximates structure-function relationships, or on small coordinate datasets, which does not scale to large datasets or handle noise. We present a novel scalable approach to efficiently discover macromolecule substructures based on three-dimensional coordinate data, without domain-specific knowledge. The approach combines structure-based frequent pattern discovery with search space reduction and coordinate noise handling. We analyze computational performance compared to traditional approaches, validate that our approach can...

4. Stochastic Cluster Dynamics of Macromolecules - Andrej Yu. Chikishev,Werner Ebeling,Aleksej V. Netrebko,Nina V. Netrebko,Youri M. Romanovsky
We study the motion of particles in a two-dimensional potentials with several minima The potential landscapes are driven by random and parametric forces. The influence of a finite size of the particles is investigated. Possible connections to proton transfer and ligand penetrations in biomolecules are discussed. I. INTRODUCTION Since the well-known paper of L.Pontryagin, A.Andronov and A.Vitt [Pontryagin et al., 1933] a lot of problems in nonlinear dynamics were considered associated with the study of transitions of multistable system from one stable state to another under the influence of noise [Hanggi et al. 1990, Talkner & Hanggi, 1995]. In recent years new problems emerged in the studies of complex vibrational...

5. Macromolecules: Origin, Development, Significance - Mark, H.
Natural polymers such as wood, cotton, wool, starch, and rubber have been known and used for a long time even though their composition and structure were unknown. At the beginning of this century systematic efforts were started to analyze these materials, elucidate their molecular pattern, and fit them into the framework of organic chemistry. It was found that they all are characterized by the presence of chain-like molecules with very high molecular weights ranging from 10000 to several millions. It was also found that these chains can be oriented by mechanical deformations and assume a laterally ordered crystal-like supermolecular arrangement....

6. Macromolecules: Origin, Development, Significance - Mark, H.
Natural polymers such as wood, cotton, wool, starch, and rubber have been known and used for a long time even though their composition and structure were unknown. At the beginning of this century systematic efforts were started to analyze these materials, elucidate their molecular pattern, and fit them into the framework of organic chemistry. It was found that they all are characterized by the presence of chain-like molecules with very high molecular weights ranging from 10000 to several millions. It was also found that these chains can be oriented by mechanical deformations and assume a laterally ordered crystal-like supermolecular arrangement....

7. Formal Language Theory and Biological Macromolecules - David B. Searls,Smithkline Beecham Pharmaceuticals
Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews languagetheoretic approaches to describing intramolecular and intermolecular structural interactions within these molecules, and evolutionary relationships between them. 1 Introduction The author has for some time been investigating the application of formal language theory to biological macromolecules, primarily nucleic acids because of the relative simplicity of the biochemical structures and interactions. After introducing the very simple mathematical foundations for these investigations, this article will review three major lines of research. These can largely be found in more fully developed form in referenced...

8. Formal Language Theory and Biological Macromolecules - David B. Searls,Smithkline Beecham Pharmaceuticals
Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews languagetheoretic approaches to describing intramolecular and intermolecular structural interactions within these molecules, and evolutionary relationships between them. 1 Introduction The author has for some time been investigating the application of formal language theory to biological macromolecules, primarily nucleic acids because of the relative simplicity of the biochemical structures and interactions. After introducing the very simple mathematical foundations for these investigations, this article will review three major lines of research. These can largely be found in more fully developed form in referenced...

9. Formal Language Theory and Biological Macromolecules - David B. Searls,Smithkline Beecham Pharmaceuticals
Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews languagetheoretic approaches to describing intramolecular and intermolecular structural interactions within these molecules, and evolutionary relationships between them. 1 Introduction The author has for some time been investigating the application of formal language theory to biological macromolecules, primarily nucleic acids because of the relative simplicity of the biochemical structures and interactions. After introducing the very simple mathematical foundations for these investigations, this article will review three major lines of research. These can largely be found in more fully developed form in referenced...

10. Teaching Electron Diffraction and Imaging of Macromolecules - Wah Chiu,Michad F. Schmid,B. V. Venkataram Prasad
Electron microscopic analysis can be used to determine the three-dimensional strutures of macromolecules at resolutions ranging between 3 and 30 . It differs from nuclear magnetic resonance spectroscopy or x-ray crystallography in that it allows an object's Coulomb potential functions to be determined directly from images and can be used to study relatively complex macromolecular assemblies in a crystalline or noncrystalline state. Electron imaging already has provided valuable stuctural information about various biological systems, including membrane proteins, protein-nucleic acid complexes, contractile and motile protein assemblies, viruses, and transport complexes for ions or macromolecules. This article, organized as a series of lectures, presents the biophysical principles of three-cdimensional analysis...

11. NURBS based B-rep Models for Macromolecules and their Properties
this paper we focus on the first case where it is required to represent the primary and secondary structure of a macromolecule. One representation of the primary structure is the space filling model, where each atom is described by a sphere with its van der Waals radius. The topological and combinatorial structure of this model has recently been explored by Edelsbrunner [9, 8, 10]. In particular from such formalization any information regarding the topological structure and the corresponding geometry of the molecule can be easily extracted. On the basis of such results we develop a B-rep data structure that aims to be useful both for visualization and modeling purposes....

12. Induction of Rules for Biological Macromolecule Crystallization - Daniel Hennessy,Vanathi Gopalakrishnan,Bruce G. Buchanan,John M. Rosenberg,Devika Subramanian
X-ray crystallography is the method of choice for determining the 3-D structure of large macromolecules at a high enough resolution. The rate limiting step in structure determination is the crystallization itself. It takes anywhere between a few weeks to several years to obtain macromolecular crystals that yield good diffraction patterns. The theory of forces that promote and maintain crystal growth is preliminary, and crystallographers systematically search a large parameter space of experimental settings to grow good crystals. There is a wealth of experimental data on crystal growth most of which is in paper laboratory notebooks. Some of the data has been gathered in electronic form, e.g., the Biological Macromolecular Crystallization Database (BMCD) which is...

13. The IMB Jena Image Library of Biological Macromolecules: 2002 update - Jan Reichert,Jrgen Shnel
The IMB Jena Image Library of Biological Macromolecules (http://www.imbjena. de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). In addition, basic information on the architecture of biological macromolecules is offered. Recent developments include a site database and an analysis tool that identifies all residues surrounding hetero components or sites according to geometrical criteria. This enables one to search for all structures with a certain pattern of amino acids/nucleotides/water adjacent to hetero components or sites. A new PDB/SWISS-PROT cross...

14. Development of Crystallization Strategies Using the Biological Macromolecule Crystallization Database - G. L. Gillil,M. Tung,J. E. Ladner
The NIST/NASA/CARB Biological Macromolecule studies requires not only finding suitable chemical agents Crystallization Database (BMCD) contains crystal data that induce and sustain crystal growth but also that those and crystallization conditions for biological parameters such as protein concentration, ionic strength, macromolecules abstracted from the literature. Each temperature, pH, etc., be sampled over a wide range of entry consists of information describing the biological values. This could require many thousands of experiments macromolecule crystallized and crystal data and the even if only a few chemical agents are used and if crystallization conditions for each crystal form. The parameters are varied with course increments. The number BMCD also serves...

15. The IMB Jena Image Library of Biological Macromolecules - Jan Reichert,Andreas Jabs,Peter Slickers,Jrgen Shnel
The IMB Jena Image Library of Biological Macromolecules (http://www.imbjena.de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). By combining automatic and manual processing it is possible to keep pace with the rapidly growing number of known biopolymer structures and to provide, for selected entries, information not available from automatic procedures. Each entry page contains basic information on the structure, various visualization and analysis tools as well as links to other...

16. Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing - Jin Kim,James R Cole,Eric Torng,Sakti Pramanik
Derivation of biological information of a macromolecule isolate based on sequence similarity is playing a significant role in numerous areas of biological research. However, it is often the case that a researcher obtains more macromolecule isolates than can be sequenced practically, due either to the high cost of sequencing or lack of specialized equipment and personnel. To overcome this difficulty, we study the problem of obtaining biological information (such as sequence information) about a macromolecule isolate using only (i) the fragmentation pattern of that isolate obtained from digestion with enzymes and (ii) a database D of sequences. We investigate a three phase approach to solving this problem. In the first phase, we obtain a restriction...

17. A Free Energy Approach to the Torsion Dynamics of Macromolecules - Sebastian Reich,Konrad-zuse Zentrum Berlin,Heilbronner Str
Based on the concept of free energy, we give a Hamiltonian formulation for the torsion dynamics of macromolecules. The appropriate reaction coordinates for the free energy calculations are defined in terms of soft constraints as introduced in [3] and [14]. We consider a few simplifications that allow one to calculate the free energy analytically and to write the corresponding equations of motion as a constrained Hamiltonian system. We also discuss a possible stochastic embedding of the reduced dynamics by means of a generalized Langevin approach. 1

18. NURBS based B-rep Models for Macromolecules and their Properties - C. Bajaj H. Y. Lee,R. Merkert V. Pascucci
this paper we focus on the first case where it is required to represent the primary structure of a macromolecule. One representation of the primary structure is the space filling model, where each atom is described by a sphere with its van der Waals radius. The topological and combinatorial structure of this model has recently been explored by Edelsbrunner [9, 10, 11]. In particular from such formalizationany information regarding the topological structure and the corresponding geometry of the molecule can be easily extracted

19. Phase Transition in the Macromolecules - Kai Xiu
this article introduced a model theory based mainly on the work of I. M. Lifshitz et al, such a theory describes with qualitative accuracy the homo-polymer chain in fairly simple situations and can, apparently, be used as a basis for further, more realistic approximations. As to biopolymers, this theory can stimulate the formation of interesting problems. References

20. Nanoribbons from conjugated macromolecules on amorphous substrates observed by SFM and TEM - Paolo Samor,Irakli Sikharulidze,Viola Francke
. Micrometre long nanoribbons have been grown from solutions of functionalized poly(para-phenyleneethynylene)s (PPE)s on noncrystalline insulating substrates including glass and carbon coated copper grids. Tapping mode scanning force microscopy (SFM) and transmission electron microscopy (TEM) revealed that these nanostructures possess a molecular cross section with a typical thickness of 2--3 molecular layers and a width which reflects the distribution of macromolecular lengths. The ribbons are therefore quite similar to the ones found on the crystalline mica substrate except that they are not oriented within the surface plane. This indicates that the growth of these architectures from solution is mainly governed by intermolecular interactions between the #-conjugated macromolecules. The possibility...

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