Links.

General: Baidu
Google
Google Scholar
CiteULike
ESI
GOPUBMED
Hubmed
Journal Citation Reports
NIH grants search tool
Pubchem
Pubmed

Email: Email-WHU
Gmail
Hotmail

Journals: NEW ENGL J MED
NAT REV MOL CELL BIO
JAMA-J AM MED ASSOC
Cell
ANNU REV BIOCHEM
Nature
NAT REV DRUG DISCOV
Science
LANCET
NAT MED
PNAS
CHEM REV
NAT BIOTECHNOL
PHARMACOL REV
ANNU REV PHARMACOL
CHEM SOC REV
CELL METAB
NAT CHEM BIOL
J EXP MED
NAT REV MICROBIOL
NAT METHODS
BRIT MED J
PLOS BIOL
MOL SYST BIOL
PLOS MED
ACCOUNTS CHEM RES
NAT STRUCT MOL BIOL
ANNU REV MED
ANGEW CHEM INT EDIT
GENOME RES
TRENDS MOL MED
PHARMACOL THERAPEUT
TRENDS PHARMACOL SCI
DIABETES
EMBO J
ADV DRUG DELIVER REV
J AM CHEM SOC
SYST BIOL
DRUG DISCOV TODAY
PLOS COMPUT BIOL
DRUG METAB REV
CHEM BIOL
AIDS
BIOESSAYS
J MED CHEM
J CHEM THEORY COMPUT
Bioinformatics
BMC BIOINFORMATICS
BMC SYST BIOL
J CHEM INF MODEL

Research Groups: KEGG
AutoDock
ZINC
UM-BBD
Systems Biology Research Group :: UCSD(Palsson)
The Systems Biology Institute (SBI)(Japan)
Prof. Douglas Kell - Bioanalytical Sciences Group
Division of Biocomputing (Dr. Tudor I. Oprea)
Cheminformatics Education: SMILES ( 3-5 Chapters)
Bioinformatics Education: 生物信息学论坛
Informatics Tools for Chemoinformatics: Fedora
Linux: Basic Commands
Python Tutorial (1-7)
Weka 3
R
Centers or Universities: Wuhan University
中国科学院上海生命科学研究院
中国科学院上海药物研究所
EBI European Bioinformatics Institute
ISB Institute of Systems Biology
SystemsX.ch The Swiss Initiative in Systems Biology
NCBI National Center for Biotechnology Information
ExPASy Proteomics server of SIB
GenomeNet
BIRD
Institute for Bioinformatics Research and Development, JST
DDBJ DNA Data Bank of Japan, NIG
DISC DNA Information and Stock Center
TIGR The Institute for Genome Research
MIPS Munich information center for protein sequences
NISTNIST
SBISBI Japan
Organizations: 中华人民共和国中央人民政府
国家自然科学基金委员会
中华人民共和国科学技术部
中华人民共和国教育部
科技型中小企业技术创新基金
东湖高新区
武汉大学东湖国家科技园
武汉国家生物产业基地 “光谷生物城”
BBSRC
Wellcome
Grand Challenges Explorations
Topics Overview- Bill & Melinda Gates Foundation.
Asthma UK
CHINA MEDICAL BOARD
News: 中华人民共和国中央人民政府
CNN
BBC
NHK
NHK WORLD Chinese
开元德国中文网
小春日本留学网（小春日本留学论坛）
未名空间
Molecules: ChemSpider Database of Chemical Structures and Property Predictions
eMolecules Chemical Structure Drawing Search
PubChem Chemical structure search | BioActivity analysis
DrugBank DrugBank
CTD The Comparative Toxicogenomics Database (CTD)
UniProt a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
PDB Protein Data Bank
ZINC
ChEBI
GenBank GenBank
MolTable MolTable
RCSB Software Tools RCSB Software Tools
TTD Therapeutic Target Database
Pathways: KEGG Kyoto Encyclopedia of Genes and Genomes
EcoCyc E. coli metabolism
BioCyc BioCyc
Reactome Reactome
EMP Enzymes and Metabolic Pathways database
BRENDA The Comprehensive Enzyme Information System
BRITE Biomolecular Reaction in Information Transmission and Expression
DIP Database of Interacting Proteins
BIND The Biomolecular Interaction Network Database
ExPASy map Biochemical Pathway by Boehringer
Metabolomics: HMDB Human Metabolome Database
Companies: Molecular Networks Molecular Networks (Prof. Johann Gasteiger)
WOMBAT World of Molecular Bioactivity (Dr. Tudor I. Oprea)
Daylight Daylight
ChemAxon ChemAxon
Symyx Symyx
Tripos Producer of sybyl, a computational tool kit for molecular design and analysis.
Accelrys Producer of various molecular modeling and simulation software for both life and materials science research (Pipeline Pilot; Discovery Studio).
Prous Science Prous Science (Thomson Reuters): Integrity
Chemical Computing Group Chemical Computing Group
Schrödinger Schrödinger
OpenEye OpenEye
Simulations Plus Simulations Plus
Reaxys Reaxys
CompuDrug CompuDrug
VLife Sciences Technologies VLife Sciences Technologies
Schrodinger Schrödinger
创腾科技有限公司 创腾科技有限公司
北京宏剑公司 北京宏剑公司
源资科技 源资科技
Spotfire Spotfire
CLC Bio CLC Bio
GeneGO GeneGO (MetaCore)
Drug Discovery Tools: Molecular Networks Molecular Networks (Prof. Johann Gasteiger)
WOMBAT World of Molecular Bioactivity (Dr. Tudor I. Oprea)
Daylight Daylight
ChemAxon ChemAxon
Symyx Symyx
Tripos Producer of sybyl, a computational tool kit for molecular design and analysis.
Accelrys Producer of various molecular modeling and simulation software for both life and materials science research (Pipeline Pilot; Discovery Studio).
Prous Science Prous Science (Thomson Reuters): Integrity
Chemical Computing Group Chemical Computing Group
Schrödinger Schrödinger
OpenEye OpenEye
Simulations Plus Simulations Plus
Reaxys Reaxys
CompuDrug CompuDrug
VLife Sciences Technologies VLife Sciences Technologies
Schrodinger Schrödinger
Spotfire Spotfire
CLC Bio CLC Bio
Amber Amber
SYBYL-X SYBYL-X
Gaussian Gaussian
Virtual Screening Links: References, Tools, Comments, Companies, Groups, Databases
Virtual screening of chemical libraries
Fragment-based drug discovery takes a virtual turn
Puzzling through fragment-based drug design
New screening tools for lead compound identification
A new school for screening
Molecular docking and ligand specificity in fragment-based inhibitor discovery
Novel 2D Fingerprints for Ligand-Based Virtual Screening
Three-Dimensional Pharmacophore Methods in Drug Discovery
Molecular Shape and Medicinal Chemistry: A Perspective
Diseases and Treatments: 新生儿呼吸窘迫综合征(NRDS) 新生儿呼吸窘迫综合征(NRDS)
固尔苏 (Curosurf) 固尔苏 (Curosurf)
珂立苏 珂立苏
珂立苏 珂立苏
人源性肺表面活性物质 人源性肺表面活性物质
Tuberculosis (TB) Tuberculosis (TB)
Diabetes Diabetes
Asthma_WhatIs Asthma_WhatIs
Asthma_Wiki Asthma_Wiki
Asthma_Sound Wave Asthma_Sound Wave
Drugs: Thalidomide 沙利度胺(反应停Thalidomide) Thalidomide (1998年沙利度胺通过了美国FDA审查并推荐应用于麻风结节性红斑。在2006年，美国FDA又审查并且通过了沙利度胺可以治疗Multiple myeloma（简称MM，又叫多发性骨髓瘤或骨髓瘤) 1991年发现它有抑制肿瘤坏死因子(TNF-α)作用 ——抗炎作用　 1994年发现它有抗血管新生作用——抗肿瘤作用
沙利度胺 沙利度胺 (沙利度胺的药理作用 　　　1．抗血管新生作用：用于抗肿瘤、血液系统疾病的治疗 　　2．免疫调节作用(抗炎作用)：用于风湿免疫性疾病、皮肤疾病的治疗 　　3．中枢神经抑制作用(镇静作用)：催眠、镇痛、止吐，抗焦虑、抗焦躁不安。 不良反应 　　　1．毒性作用：本药为强致畸药，故孕妇禁用，育龄妇女需采取有效避孕措施方可应用。停药6个月以上方可怀孕。一般发生在妊娠前3个月，尤其是第45～55天。但并非在服药期间均发生畸形。无骨髓抑制，无肝肾、心肺、大脑等毒性报道。至今半死量没有测出，不引起慢性中毒。 　　此药不影响服药者的生殖器官，而是通过胎盘直接作用于敏感期的胚胎，小剂量即可致畸。因此，育龄妇女要禁用。 　　长期大剂量使用本品(40g以上)可出现多发性神经炎，感觉异常等现象。一旦出现应即停药，约25％完全恢复，25％好转或部分恢复，还有50％停药4～5年后仍不恢复。 　　2．其他不良反应：常见镇静作用，嗜睡、困倦、头晕、头痛，便秘、口干、皮疹、皮肤干燥、四肢水肿等;食欲亢进、恶心、深静脉血栓、低血压、心律过慢(<60次/分)等少见。大部分均轻微并可以耐受，停药后可以消退。 ) 作用机理 据2010年3月12日的《科学》杂志报道说，在一项可能会带来较为安全的thalidomide另选药物开发的研究中，日本的研究人员如今发现了 thalidomide是如何使发育中的肢体发生畸变的。 尽管科学家们曾经提出过许多的假说，但该药的作用机制在此之前一直是一个谜。用斑马鱼和小鸡作为动物模型，Takumi Ito及其同僚发现，thalidomide会与蛋白质cereblon结合。这种相互作用会抑制cereblon的酶活性，而这种活性对肢体的发育是重要的。文章的作者提出，有可能设计出可避免这种效应的thalidomide的衍生物。 除了致畸性，沙利度胺还有弱致癌性，可能的不良反应还包括外周神经炎、麻痹、感觉异常、意识混乱、低血压等。
Lenalidomide Lenalidomide
Docking: Docking Docking
DockingServer DockingServer
installation_of_autodock installation_of_autodock
Docker Docker
Software_Docking Software_Docking
PDB PDB
Zinc Zinc
docking 时蛋白质中水的问题 docking 时蛋白质中水的问题
Prepare PDB file for docking programs Prepare PDB file for docking programs
Computer Software Resources: SVN SVN
SVN Book SVN Book
Command Line SVN Tutorial Command Line SVN Tutorial
IP Locator IP Locator
Education Resources: 一是做事必须勤奋；二是锲而不舍，有始有终；三是一定要有好帮手；四是待人忠实，做事雷厉风行。 bioseminars bioseminars
PFAM PFAM
Sequence_motif Sequence_motif
Structural motif Structural motif
PROSITE Database of protein domains, families and functional sites
CATH CATH
SCOP SCOP: Structural Classification of Proteins
Protein_structure_prediction Protein_structure_prediction
WhiteWater的化学信息学博客 WhiteWater的化学信息学博客
世界名牌大学课件下载地址 世界名牌大学课件下载地址
Biosynthesis Resources: biofab biofab
Stanford's Department of Bioengineering Stanford's Department of Bioengineering
Department of Bioengineering at UC Berkeley Department of Bioengineering at UC Berkeley
Joint BioEnergy Institute Joint BioEnergy Institute
SynBERC SynBERC
Berkeley Lab Berkeley Lab
The BioBricks Foundation (BBF) The BioBricks Foundation (BBF)
QB3 QB3
Jay D. Keasling Jay D. Keasling
Adam Arkin Adam Arkin
Molecular Biosciences, ICL Molecular Biosciences, ICL
systemsbiology, ICL systemsbiology, ICL
Resources copy from Prof. Tang's group:

数据库

 

蛋白质序列库PIR

http://pir.georgetown.edu/  

基因序列库GenBank

http://www.ncbi.nlm.nih.gov/Genbank/index.html  

京都基因大全KEGG

http://www.genome.jp/kegg/

蛋白质结构数据库PDB

http://www.rcsb.org/pdb/  

核酸结构数据库NDB

http://ndbserver.rutgers.edu/

潜在药物靶标数据库PDTD

http://www.dddc.ac.cn/pdtd/   

蛋白质－配体结合数据库BindingDB

http://www.bindingdb.org/bind/index.jsp

NIH小分子数据库PubChem

http://pubchem.ncbi.nlm.nih.gov/

商用化合物数据库ZINC

http://zinc.docking.org/

药物数据库DrugBank

http://www.drugbank.ca/

毒性数据网络TOXNET

http://toxnet.nlm.nih.gov/

 

 

在线服务

 

蛋白质序列检索SWISS-PROT

http://www.expasy.ch/sprot/

同源模板检索BLAST

http://www.ncbi.nlm.nih.gov/BLAST/  

同源模板检索Fasta

http://www.ebi.ac.uk/Tools/fasta33/index.html

序列比对ClustalW

http://www.ebi.ac.uk/Tools/clustalw2/index.html

蛋白质结构预测PredictProtein

http://www.predictprotein.org/

同源模拟SWISS-MODEL

http://swissmodel.expasy.org/SWISS-MODEL.html

蛋白质结构分析Prosa

https://prosa.services.came.sbg.ac.at/prosa.php

反向分子对接TarFisDock

http://www.dddc.ac.cn/tarfisdock/index.php

药代动力学及毒性预测PreADMET

http://preadmet.bmdrc.org/

小分子性质计算

http://www.molinspiration.com/cgi-bin/properties

小分子LogP值计算

http://www.vcclab.org/lab/alogps/start.html

分子描述符计算E-Dragon

http://www.vcclab.org/lab/edragon/start.html

NCI小分子数据库在线检索

http://cactus.cit.nih.gov/ncidb2/

 

 

免费软件

 

格式转换软件Babel

http://openbabel.org/wiki/Main_Page

分子编辑器JME

http://www.molinspiration.com/jme/

同源模建软件Modeller

http://salilab.org/modeller/

分子显示软件RasMol

http://www.rasmol.org/

分子显示软件PyMol

http://www.pymol.org/

分子显示软件DeepView

http://spdbv.vital-it.ch/

分子显示软件VMD

http://www.ks.uiuc.edu/Research/vmd/

分子动力学软件Gromacs

http://www.gromacs.org/

分子动力学软件NAMD

http://www.ks.uiuc.edu/Research/namd/

分子动力学软件Amber

http://ambermd.org/

分子对接软件DOCK

http://dock.compbio.ucsf.edu/

分子对接软件AutoDock

http://autodock.scripps.edu/

量子化学软件GAMESS

http://www.msg.chem.iastate.edu/gamess/

 

 

综合位点及专业BBS论坛

 

计算化学CCL

http://www.ccl.net/

虚拟计算化学实验室VCCLab

http://www.vcclab.org/

QSAR世界

http://www.qsarworld.com/index.php

分子模拟论坛

http://www.mdbbs.org/

小木虫论坛

http://emuch.net/bbs/

Nobel论坛

http://www.i-nobel.com/bbs/

CHARMM论坛

http://www.charmm.org/ubbthreads/ubbthreads.php?Cat=0

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