Dear friends: Do you know how to find out database quickly without
entering so many university libraries and search the web again and
again? Do you know what databases does a library have? You will
recommend google search engine, but does it provide you enough and
prcise information? No!So this handbook for you guys as an index of
library resource menu, for you to get to any database or journal
without entering lots of university librares. contact:
www.passfans. com
الاثنين، 21 أبريل 2008
الخميس، 17 أبريل 2008
Techniques for Searching Databases of Three-Dimensional (3D) Structures with Receptor-Based Queries
Ligand-based vs. Receptor-based 3D Searching
A key concept in 3D searching is the pharmacophore. The term, introduced by Ehrlich in the early 1900s , refers to the molecular framework that carries (phoros) the essential features responsible for a drug's (pharmacon) biological activity. In the current literature, the term has been expanded to refer to the 3D arrangement of functional groups that enable a compound to exert a particular biological effect. Due to stereochemical considerations (i.e., three-point attachments), many pharmacophores are defined simply in terms of three atoms and three distances. If more information is available, other geometric objects and constraints can be added, including constraints on data associated with atoms and bonds . Presently, most pharmacophores are defined in terms of the atoms and bonds of the ligand structures. This ligand-based definition has advantages for input and searching purposes; in the case where the structure of the receptor is completely unknown, it is the only way one can effectively define a pharmacophore model.
It is clear that drugs that bind to a common receptor do not necessarily bind with similar functional groups precisely overlapped; rather, these drugs may show multiple modes of binding . The interactions between a drug molecule and a receptor can be dispersed and nonspecific, as in steric and lipophilic interactions - which nevertheless account for most of the free energy changes in binding . Alternatively, they can be highly specific and directional, such as interactions involving H-bond donors and acceptors or those with bound metal ions. But even then, precise overlap of heteroatoms may not result, since the specific interactions occur over a range of angles, distances, and energies .
Clearly, in such cases, a receptor-based approach to a pharmacophore definition is needed to carry key features of the receptor involved in drug molecule binding. A full receptor-based pharmacophore model complements the ligand-based pharmacophore model for the same activity; it is the 'lock' for a given 'key.' This concept has been expressed and utilized previously, as in the extended molecule approach of Andrews . Our purpose is to show how to implement receptor-based queries in a pharmacophore-based 3D search system. We will also evaluate the success of these queries with respect to their pharmacophoric counterparts by testing them on a database of drugs with known activities.
A key concept in 3D searching is the pharmacophore. The term, introduced by Ehrlich in the early 1900s , refers to the molecular framework that carries (phoros) the essential features responsible for a drug's (pharmacon) biological activity. In the current literature, the term has been expanded to refer to the 3D arrangement of functional groups that enable a compound to exert a particular biological effect. Due to stereochemical considerations (i.e., three-point attachments), many pharmacophores are defined simply in terms of three atoms and three distances. If more information is available, other geometric objects and constraints can be added, including constraints on data associated with atoms and bonds . Presently, most pharmacophores are defined in terms of the atoms and bonds of the ligand structures. This ligand-based definition has advantages for input and searching purposes; in the case where the structure of the receptor is completely unknown, it is the only way one can effectively define a pharmacophore model.
It is clear that drugs that bind to a common receptor do not necessarily bind with similar functional groups precisely overlapped; rather, these drugs may show multiple modes of binding . The interactions between a drug molecule and a receptor can be dispersed and nonspecific, as in steric and lipophilic interactions - which nevertheless account for most of the free energy changes in binding . Alternatively, they can be highly specific and directional, such as interactions involving H-bond donors and acceptors or those with bound metal ions. But even then, precise overlap of heteroatoms may not result, since the specific interactions occur over a range of angles, distances, and energies .
Clearly, in such cases, a receptor-based approach to a pharmacophore definition is needed to carry key features of the receptor involved in drug molecule binding. A full receptor-based pharmacophore model complements the ligand-based pharmacophore model for the same activity; it is the 'lock' for a given 'key.' This concept has been expressed and utilized previously, as in the extended molecule approach of Andrews . Our purpose is to show how to implement receptor-based queries in a pharmacophore-based 3D search system. We will also evaluate the success of these queries with respect to their pharmacophoric counterparts by testing them on a database of drugs with known activities.
الجمعة، 11 أبريل 2008
Learning Chemistry Online
Chemistry is one of those hands on subjects that is probably extremely hard to Learn online. Though, I have run in to some pretty neat lessons around the internet that can teach you some general chem knowledge. Do you think high school students would enjoy this kind of thing? Or to expand on that, do you think they could use these kind of online educational resources as a homework tool?
Here is a pretty cool lesson:
http://learnhub.com/lesson/page/118-creating-colored-flames
Here is a pretty cool lesson:
http://learnhub.com/lesson/page/118-creating-colored-flames
Check out Tripos Discovery Drugs
www.tripos.com
Well-designed and frequently updated software can save valuable time
and often means the difference between success and failure. Tripos'
premier computational informatics offering, SYBYL, leads the way in
innovation with its ever-growing suite of technologies and our
commitment to applied science and frequent product enhancements
Surflex-Dock
Ligand-Receptor Docking and Virtual Screening
Now Available Fully Integrated with SYBYL® 7.2!
Overview
Screening large compound libraries remains an expensive and time-
consuming task. Computational high-throughput screening can enrich
the fraction of suitable compounds in a screening collection,
thereby reducing the cost of biological testing in lead discovery.
Surflex-Dock offers unparalleled enrichments in virtual high-
throughput screening combined with state-of-the-art speed, accuracy
and usability. It uses an updated and re-parameterized empirical
scoring function (based on the Hammerhead docking system) with
additional negative training data and a search engine that relies on
a surface-based molecular similarity method.
Surflex-Dock has been extensively validated and favorably compared
to all leading competing methods by independent researchers
(Kellenberger et al., (2004) Proteins: Structure, Function, and
Bioinformatics 57, 225-242), along with 28 other studies by the
applications author, Prof. Ajay N. Jain, Ph.D., a faculty member at
the University of California San Francisco Cancer Research
Institute.
"Surflex-Dock couples a unique scoring function with a patented
state-of-the-art search engine. The combination has been shown to
yield excellent results in terms of docking accuracy, and
distinctively superior results in terms of screening enrichment,"
said Prof. Ajay N. Jain.
DISCOVERY INFORMATICS
SYBYL®
Benchware®
Informatics Research Center
Platform Technologies
Informatics Services
DISCOVERY RESEARCH
LeadDiscovery™
Discovery Chemistry
Screening Libraries
Research Partnerships
Knowledge-Driven Process
Well-designed and frequently updated software can save valuable time
and often means the difference between success and failure. Tripos'
premier computational informatics offering, SYBYL, leads the way in
innovation with its ever-growing suite of technologies and our
commitment to applied science and frequent product enhancements
Surflex-Dock
Ligand-Receptor Docking and Virtual Screening
Now Available Fully Integrated with SYBYL® 7.2!
Overview
Screening large compound libraries remains an expensive and time-
consuming task. Computational high-throughput screening can enrich
the fraction of suitable compounds in a screening collection,
thereby reducing the cost of biological testing in lead discovery.
Surflex-Dock offers unparalleled enrichments in virtual high-
throughput screening combined with state-of-the-art speed, accuracy
and usability. It uses an updated and re-parameterized empirical
scoring function (based on the Hammerhead docking system) with
additional negative training data and a search engine that relies on
a surface-based molecular similarity method.
Surflex-Dock has been extensively validated and favorably compared
to all leading competing methods by independent researchers
(Kellenberger et al., (2004) Proteins: Structure, Function, and
Bioinformatics 57, 225-242), along with 28 other studies by the
applications author, Prof. Ajay N. Jain, Ph.D., a faculty member at
the University of California San Francisco Cancer Research
Institute.
"Surflex-Dock couples a unique scoring function with a patented
state-of-the-art search engine. The combination has been shown to
yield excellent results in terms of docking accuracy, and
distinctively superior results in terms of screening enrichment,"
said Prof. Ajay N. Jain.
DISCOVERY INFORMATICS
SYBYL®
Benchware®
Informatics Research Center
Platform Technologies
Informatics Services
DISCOVERY RESEARCH
LeadDiscovery™
Discovery Chemistry
Screening Libraries
Research Partnerships
Knowledge-Driven Process
الاثنين، 7 أبريل 2008
Virtual Textbook of Organic Chemistry
very interesting site about basic organic chemistry hope to make use of it
http://www.cem.msu.edu/%7Ereusch/VirtualText/intro1.htm
http://www.cem.msu.edu/%7Ereusch/VirtualText/intro1.htm
Online degrees & courses
There are many choices available and this is right aproach that first research about degree and than get one.
Master, Bachelor, Associate and Phds:
http://www.degreexs .com/?aff= 4837
http://courtneytuttle.com/2007/02/25/starting-a-blog-in-5263-words/
Master, Bachelor, Associate and Phds:
http://www.degreexs .com/?aff= 4837
http://courtneytuttle.com/2007/02/25/starting-a-blog-in-5263-words/
الثلاثاء، 1 أبريل 2008
Teaching Style
Teaching Style
In education generally (in the UK and elsewhere) there seems to be a swing back to "traditional" methods of teaching. The progressive ideas that evolved from the self-discovering sixties are giving way to a more pedagogical style. Whilst this approach may well be appropriate to junior & intermediate levels, particularly in the sciences, students in higher education still need to be encouraged to think for themselves if society wishes properly to develop its human and environmental resources.
The Chemistry Education: Research and Practice site offers very interesting articles on this theme. The following extract from the paper by Uri Zoller is found particularly pertinent:-
Environmental sciences are emerging as a new interdisciplinary scientific “discipline”, … within a process of distancing from specialized, compartmentalized, and disciplinary, into multidimensional, cross-boundary endeavor in the science-technology-environment society (STES) interfaces. This poses new challenges with respect to the intrinsic science and technology organization and to the way the relevant knowledge and processes will be put into action …
The essence of the current reform in science/chemical education, worldwide, is a paradigm shift from algorithmic/imparting knowledge-type teaching to higher-order cognitive skills (HOCS) learning. In the context of education in environmental chemistry (EEC), the ultimate target is the STES-literate graduate, capable of evaluative thinking, decision making, problem solving and taking a responsible action accordingly. …
…Environmental literacy requires the integration of environmental sciences into core chemical courses as well as the development and implementation of HOCS-promoting teaching strategies and assessment methodologies in chemical education …(and) The development of students’ HOCS for transfer, followed by assessment of ‘HOCS performance’; is the task ahead for meaningful EEC…
…
Ensuring sustainable development requires, .. a radical change in the “environmental behavior” and “thinking environment” of individuals, groups, institutions, industry, social organizations, politicians, and governments. Therefore, HOCS learning constitutes a prerequisite. … The question is how to contribute to this end in the context of chemistry and environmental education.
In view of the above, a ‘call for papers’ for a special Theme Issue of Chemistry Education: Research and Practice (CERP) was issued, inviting contributions on the theme of chemistry and environmental education of two kinds: (a) research based; (b) practice-oriented papers …
…
This peer-reviewed Special Theme Issue .. consists of seven papers, contributed by Eichler, Lubezky, Morgil, Petrou, Schallies, Scoullos, Tal et al., constituting a spectrum of appropriate responses to the above subjects in different contexts. As such, they contribute meaningfully, so we believe, to the research, theory and practice in chemistry and environmental education, education in environmental chemistry and STES-oriented science education. The time is ripe for taking action accordingly in chemistry education.
In education generally (in the UK and elsewhere) there seems to be a swing back to "traditional" methods of teaching. The progressive ideas that evolved from the self-discovering sixties are giving way to a more pedagogical style. Whilst this approach may well be appropriate to junior & intermediate levels, particularly in the sciences, students in higher education still need to be encouraged to think for themselves if society wishes properly to develop its human and environmental resources.
The Chemistry Education: Research and Practice site offers very interesting articles on this theme. The following extract from the paper by Uri Zoller is found particularly pertinent:-
Environmental sciences are emerging as a new interdisciplinary scientific “discipline”, … within a process of distancing from specialized, compartmentalized, and disciplinary, into multidimensional, cross-boundary endeavor in the science-technology-environment society (STES) interfaces. This poses new challenges with respect to the intrinsic science and technology organization and to the way the relevant knowledge and processes will be put into action …
The essence of the current reform in science/chemical education, worldwide, is a paradigm shift from algorithmic/imparting knowledge-type teaching to higher-order cognitive skills (HOCS) learning. In the context of education in environmental chemistry (EEC), the ultimate target is the STES-literate graduate, capable of evaluative thinking, decision making, problem solving and taking a responsible action accordingly. …
…Environmental literacy requires the integration of environmental sciences into core chemical courses as well as the development and implementation of HOCS-promoting teaching strategies and assessment methodologies in chemical education …(and) The development of students’ HOCS for transfer, followed by assessment of ‘HOCS performance’; is the task ahead for meaningful EEC…
…
Ensuring sustainable development requires, .. a radical change in the “environmental behavior” and “thinking environment” of individuals, groups, institutions, industry, social organizations, politicians, and governments. Therefore, HOCS learning constitutes a prerequisite. … The question is how to contribute to this end in the context of chemistry and environmental education.
In view of the above, a ‘call for papers’ for a special Theme Issue of Chemistry Education: Research and Practice (CERP) was issued, inviting contributions on the theme of chemistry and environmental education of two kinds: (a) research based; (b) practice-oriented papers …
…
This peer-reviewed Special Theme Issue .. consists of seven papers, contributed by Eichler, Lubezky, Morgil, Petrou, Schallies, Scoullos, Tal et al., constituting a spectrum of appropriate responses to the above subjects in different contexts. As such, they contribute meaningfully, so we believe, to the research, theory and practice in chemistry and environmental education, education in environmental chemistry and STES-oriented science education. The time is ripe for taking action accordingly in chemistry education.
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