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ganchao1776至尊木虫 (职业作家)
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[交流]
介绍一个查看蛋白质三维结构的好软件
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软件的名称是pymol，在百渡上搜一下就能找到下载的地方，我当初就是这么下载一下来，有10多M大小，传不上来，实在不好意思！！ 该软件是用来观看pdb格式的不错软件，可以提供多种模式观看蛋白质三维结构，有幸趣的可以下下来试一下，对搞蛋白分子改造研究的非常有用，如果你要写蛋白分子改造方面的论文，它会使你的文章增光不少！！ |
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gtj19731003
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2楼2007-04-01 22:37:16
ganchao1776
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3楼2007-04-03 21:34:41
ganchao1776
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4楼2007-04-03 21:56:34
5楼2007-04-03 23:52:37
ganchao1776
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6楼2007-04-04 14:40:49
7楼2007-04-04 23:52:41
yalefield
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PyMOL是用Python语言开发的FOSS (Free and Open Source Software)。 作者Warren L. DeLano曾经跟老汉抱怨说： 用PyMOL制作的、漂亮的、印刷质量的分子结构图， 频繁地出现在Nature、Science等科技期刊上， 但是，却从来没有人把PyMOL作为参考文献引用。 如果有这个引用的话，PyMOL将是几十年来引用率最高的“文献”(之一)！ 这也是科研软件开发者的悲哀。 作者Warren L. DeLano创立了DeLano Scientific公司 联系地址： P.O. Box 1118 Palo Alto, CA 94302-1118 U.S.A. 除了PyMOL之外，FreeMOL是DeLano Scientific公司的一个宏伟的作品： http://www.bioinformatics.org/freemol/ FreeMOL Home Page Introduction Many computational tools exist for biomedical research from both commercial, academic, and free sources. However, we lack a set of standard assumptions necessary for creating software systems that effectively combine diverse components. The FreeMOL Project is an attempt to meet this need through specification of a minimal set of common assumptions that will enable construction of systems which reliably combine multiple components from a variety of sources. What are the FreeMOL Assumptions? The FREEMOL environment variable contains the root directory for FreeMOL. A csh-based command shell is present in /bin/csh. A minimal set of tools from the Free Software Foundation are in the path. Compilers for building packages are in the path. Notes The $FREEMOL directory is designed to be a user-space equivalent of /usr/local. Users should not need to be root in order to install and utilize FreeMOL packages. Most packages require some kind of environment variable or path configuration. FreeMOL provides a standard and robust mechanism for establishing such prerequisites. FreeMOL requires GNU-make and a few other common tools. Each packages may have its own compiler dependencies. A C compiler is essential, C++ and Fortran compilers will be needed in many cases. What is the FreeMOL Distribution? The FreeMOL distribution ("freemol" CVS tree) consists of a FreeMOL directory skeleton and associated Makefile and scripts capable of building FreeMOL packages on multiple platforms from pristine source distributions (gzipped tarballs of specific versions). In addition to the "freemol" distribution, there is a "freemol-src" CVS tree which contains compressed copies of all the pristine source files for FreeMOL packages which can be legally redistributed. How Will This Help? Because FreeMOL packages are autoconfigured in a consistent manner, naive users will be able to install a collection of interoperable software in a matter of minutes from source code without any manual reconfiguration. Once installed, programs and scripts will be able to call one another in a reliable manner to conduct complex tasks involving multiple components. What Platforms Will Be Supported? FreeMOL holds that cross-platform compatability is athe responsibility of the package, not the distribution. For now, x86 Linux will be the primary target platform, but the package Makefiles are constructed in such a way as to enable divergent building procedures on different platforms. |
8楼2007-04-05 00:20:39
yalefield
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Warren L. DeLano的介绍 [转]
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By day, Dr. Warren L. DeLano is an informatics scientist for Sunesis Pharmaceuticals. By night, Warren is an open-source software developer. His lead project, PyMOL, is the most powerful molecular graphics package currently available as completely unrestricted open-source software. It is also one of very few high-performance molecular graphics packages to support a native Python API. DeLano's mission is to develop high-impact biopharmaceutical software. As a student and scientific programmer at Yale University, he was a developer of the popular X-PLOR and CNS programs for structural biology. DeLano obtained his Ph.D. in Biophysics from the University of California, San Francisco in 1999. He performed the bulk of his graduate research at Genentech, Inc. under the supervision of Dr. Jim Wells. DeLano used phage display, X-ray crystallography, and computational tools to study the origins of binding energy in protein interfaces. He developed the RigiMOL program to analyze conformational changes in protein interfaces, and SiteFinder to study properties of protein surfaces. In 1998, DeLano left Genentech to help Jim Wells launch Sunesis Pharmaceuticals, Inc. a company focused on exploiting energetic "hot spots" on proteins for purposes of drug-discovery. Over the past three years, DeLano has led the development of informatics and IT infrastructure at Sunesis, where open-source components played a major role, from deployment of Linux servers and a Linux computing cluster, to creation of a Python-based chemical informatics platform. DeLano believes that the pharmaceutical industry has a tremendous but largely unrealized interest in supporting open-source software development. |
9楼2007-04-05 00:22:48
yalefield
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Warren L. DeLano在O'Reilly会议的讲话 [转]
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O'Reilly是世界上著名的信息产业与开源软件、书籍出版商。 Warren L. DeLano作为Sunesis Pharmaceuticals的代表，在O'Reilly主办的生物信息学技术会议上讲话：“开放性的生物药学计算环境” O'Reilly Bioinformatics Technology Conference January 28-31, 2002 -- Tucson, AZ -------------------------------------------------------------------------------- Session PyMOL & FreeMOL: Leveraging Molecular Visualization to Create an Open Biopharmaceutical Computing Environment Warren L. DeLano, Informatics Scientist, Sunesis Pharmaceuticals Track: Bioinformatics.org Date: Wednesday, January 30 Time: 3:00pm - 3:45pm Location: Canyon III While many essential computational tasks in drug discovery can now be accomplished with free or open-source components, there is currently no context where such components might be effortlessly combined to carry out complex multi-step procedures in molecular modeling and informatics. The FreeMOL project aims to establish this context by implementing a minimal set of common assumptions that will nucleate the world's first open-source molecular operating environment for drug-discovery. The open-source, anchoring visualization component, molecular graphics program PyMOL will be used to catalyze the creation of FreeMOL, while FreeMOL components are integrated. However, since FreeMOL is merely a set of assumptions held together with dynamic scripting languages like Python and Perl, PyMOL will eventually be just another interchangeable component in the FreeMOL suite of interoperable tools. When complete, FreeMOL will contain capabilities comparable to commercial software suites, including molecular visualization, drawing, clean up, energy minimization, dynamics, searching, storage, enumeration, docking, electrostatics, sequence alignment, homology modeling, and so forth. Plus, FreeMOL will serve as an open conduit for integrating diverse commercial software packages, thus eliminating the need for the many redundant integrative development efforts currently ongoing throughout the industry. As an open-source alternative to commercial software suites, FreeMOL will benefit research in academia and industry by greatly increasing the amount of computational Science, which can be done with minimal expense. Also, by providing competition to commercial packages, FreeMOL will bring about a decrease in price and an increase in the quality of commercial tools. |
10楼2007-04-05 00:28:15