我不是“高手”，对于计算机辅助药物设计来说，只是一个初学者，在这里我会把我所知道的写下来与大家交流，希望能结交众多志同道合的朋友。这里要特别感谢biolover的alchemy,biohity曾经给我的帮助，他们是我心目中真正的高手。
1. 做生物大分子结构的pc机配置
转自biolover biohity的推荐配置
1. 二手主板Tyan(泰安) Tiger MPX S2466N-4M 加两个Athlon MP 2400+ (是用XP 1700+改装的）。总共3900元
2. 二手野猫4110显卡：$110.00 + ￥160关税。（未用上，因AGP口不配）。改用Synergy II显卡：250元
3. 二手DC390U3W的SCSI卡：800元
4. 36G日立全新硬盘：1100元
5. SGI 1600SW 原装、全新液晶monitor：$1200 ＋ ￥1500（关税）
6. 美基P4-450瓦电源：450元；月光机箱：350元
7. 内存 512M;
8. 系统：win2000及Linux（在不同的硬盘上）。RedHat 7.2。
SGI的机子也很容易在国内买到极好的二手。O2-5K-200Mhz大约2100元即可买到。Octane-R12k-300Mhz则贵些。但ebay上只要$300～400即可。PC机是无法与这类机子相提并论的。要知道，1999年时，上述Octane要卖两万美元啊！
1、如果你在上海，进入易趣网站www.eachnet.com，在电脑-->工作站或服务器的栏目下，找ninjaa这个人即可。
2、如果你在北京， http://www.qianye.y365.com/newpage5.html 并电话联系即可，此人有Octane的各种机子卖，但要价太贵。
3、美国ebay上较便宜，但每台进口的Octane要交400元人民币左右的关税

转：一步一步学计算机辅助药物设计[二]
一步一步学计算机辅助药物设计v1.0
来源：生物信息论坛 www.bioin.org 2003.4.18
发贴人：qianfeng； 整理人：lyover

转：一步一步学计算机辅助药物设计[二]

2. 再看看相关的教材和期刊
(1)入门教材
biolover Alchemy推荐
Hyperchem里有一本书，叫“Computational Chemistry”，个人觉得比较经典。以前是独立出来的PDF，现在集成到27M/2700页的大个头里面了。
刘次全 编过一本“量子生物学”，随后编了“结构生物学”等，呵呵，神人
BioMedCAChe的UserGuide是比较通俗的
(2)推荐使用软件
Hyperchem，ICM，BioMedCAChe
(3)相关的部分专业期刊
转自biolover biotech_lqh发贴
DDT（drug discovery today)
http://www.drugdiscoverytoday.com/
PROTEINS-STRUCTURE FUNCTION AND GENETICS
http://journals.wiley.com/0887-3585/
BIOINFORMATICS
http://bioinformatics.oupjournals.org/
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEIN STRUCTURE AND MOLECULAR ENZYMOLOGY
http://www.elsevier.com/locate/issn/01674838
JOURNAL OF MEDICINAL CHEMISTRY
http://pubs.acs.org/journals/jmcmar/index.html
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
http://www.kluweronline.com/issn/0920-654X/contents
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
http://pubs.acs.org/journals/jcisd8/index.html
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
http://www.elsevier.nl/locate/inca/525012
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS http://www.jbsdonline.com/

一步一步学计算机辅助药物设计[三]

3. 还得熟悉一下有哪些大公司
开发分子模拟软件的一些公司及其网址
Tsar 、CAChe、Chem-X、UniChem、AMBER 、AMSOL 、AutoDock Oxford Molecular公司 http://www.oxmol.com/
Cerius2 、InsightII、WebLab、Catalyst、FELIX、QUANTA Molecular Simulations Inc. (MSI) 公司 http://www.msi.com/
SYBYL, CoMFA, Biopolymer, TRIAD, GeneFold, MOLCAD, Alchemy Tripos
公司 http://www.tripos.com/
ChemDraw, Chem3D,ChemFinder,CambridgeSoft (CS)公 http://www.camsoft.com/
Gaussian Gaussian, Inc. 公司 http://www.gaussian.com/
SPARTAN、TITAN Wavefunction, Inc公司 http://www.wavefun.com/
PCMODEL Serena Software公司 http://www.serenasoft.com/
MOPAC Fujitsu Ltd.公司 http://www.fujitsu.com/
Conformer Princeton Simulations公司 http://www.conformer.com/

一步一步学计算机辅助药物设计[四]

4. 开讲了，先讲讲分子对接，这里主要是指有机分子和受体的对接
受体当然是蛋白，有晶体结构的话，先学学PDB的格式(略)
蛋白结构模拟全攻略
1 先熟悉一下几个蛋白结构的数据库
Protein Structure Databases. Comparison and Classification of Protein Structures.
The study, comparison and classification of the already known protein structures allows to extract information about sequence/family/structure relationships that can be used latter for predictions.

PDB. The database of protein structures. http://www.rcsb.org/
PDBsum. Summaries and structural analysis of PDB files.
http://www.biochem.ucl.ac.uk/bsm/pdbsum/
OCA. Integration of PDB with other sources of data. http://oca.ebi.ac.uk/
SCOP. Human expert classification of protein structures.
http://scop.mrc-lmb.cam.ac.uk/scop/
FSSP(Dali). Automatic classification. http://www.ebi.ac.uk/dali/
CATH. Semi-automatic classification.
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
2 对于从来没做过结构的新手，可以看这里
The structure prediction Meta Server
http://bioinfo.pl/meta/
The structure prediction Meta Server offers a gateway to many high quality fold recognition servers and provides and infrastructure and main interface to several highly reliable consensus methods. The Meta Server represents the firs step in the our fold prediction strategy.
这是个大杂烩，是不是用了它其他的都不用了？ ；）
3 如果想多了解几个基于web的结构预测网站，可以看看这些
Web-based Comparative Protein Modelling Resources
SwissModel
http://www.expasy.ch/swissmod/
SWISS-MODEL is an Automated Protein Modelling Server running at GlaxoSmithKline in Geneva (Switzerland) and the Advanced Biomedical Computing Center (NCI, Frederick MD).
CPHModels
http://www.cbs.dtu.dk/services/CPHmodels/
Protein structure prediction server using distance constraints.
Center for Biological Sequence Analysis. (The Technical University of Denmark, Denmark).
SDSC1
http://cl.sdsc.edu/hm.html
San Diego Supercomputer Center Protein Structure Homology Modeling Server
3D-JIGSAW
http://www.bmm.icnet.uk/servers/3djigsaw/
3D-JIGSAW is an automated system to build three-dimensional models for proteins based on homologues of known structure.
ESyPred3D
http://www.fundp.ac.be/urbm/bioinfo/esypred/
ESyPred3D is an Expert System for the Prediction of proteins 3D structures running at the University of Namur (Belgium). The specificity of ESyPred3D is the building of the target-template alignment by combining several alignment programs.
Pcomb-Pcons
http://www.sbc.su.se/~arne/pcomb/
Pcomb-Pcons uses a combination of several sequence-profile and profile-sequence searches. It produces both homology modelling models and alignments.
Web-based Threading Resources
3D-PSSM
http://www.sbg.bio.ic.ac.uk/~3dpssm/
Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information.
FUGUE
http://www-cryst.bioc.cam.ac.uk/~fugue/
The program FUGUE searches a sequence or sequence alignment against the library of profiles. Environment-specific substitution tables were derived from the structure-based alignments in the HOMSTRAD database. Each alignment in HOMSTRAD was converted into a scoring template (profile) using the environment-specific substitution tables and environment-dependent gap penalties.
123
http://123d.ncifcrf.gov/
Libellula
http://www.pdg.cnb.uam.es:8081/libellula.html
SAMt99
http://www.cse.ucsc.edu/research ... library-search.html
SAUSAGE
http://rsc.anu.edu.au/~arussell/TheSausageMachine.html
Sausage (Sequence-structure Alignment Using a Statistical Approach Guided by Experiment) is a protein threading program.
Superfamily
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/index.html
Protein domain assignments to SCOP structural superfamilies using a hidden Markov model library.
bioinbgu
http://www.cs.bgu.ac.il/~bioinbgu/form.html
4 如果想看看预测后的结果，可以用一下Swiss-PdbViewer
同源模拟之swiss-model
SWISS-MODEL
http://www.expasy.org/swissmod/SWISS-MODEL.html
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.

Swiss-PdbViewer
http://www.expasy.org/spdbv/mainpage.htm
a tool for viewing and manipulating protein structures and models (Macintosh, PC, SGI and Linux).
非常容易上手，适合初学者使用，有详细的说明，以及邮件列表可以咨询
5 如果觉得想自己动手，模拟一个，可以试试modeller
同源模拟之modeller
MODELLER
据说是目前最好的同源模拟软件
http://salilab.org/modeller/
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (2, 3), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is written in Fortran 90 and runs on the Pentium PC's (Linux and Win XP), Apple Macintosh (OS X) and workstations from Silicon Graphics (IRIX), Sun (Solaris), IBM (AIX), and DEC Alpha (OSF/1).
6 模拟完得评价一下,不过这有些难度,我是没搞懂,请哪位大侠指点指点
Model Evaluation.
Once a model has been generated, these tools allow to evaluate its quality.
EVA
http://maple.bioc.columbia.edu/eva/
EVA continously and automatically analyses protein structure prediction servers in 'real time' Columbia & Rockefeller Univ, New York.
Biotech Validation Suite.
http://biotech.embl-heidelberg.de:8400/
Based on the tools implemented in the WhatIf program.
WhatCheck / WhatIf Gert
http://www.cmbi.kun.nl/whatif//
ProSA II.
http://www.came.sbg.ac.at/Services/prosa.html
小结:其实模拟软件有很多，用的不同算法，各有优缺点，还有更专业的，专业的一般都是Unix下的，象我这样的初级用户是不用想了 返回小木虫查看更多