Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and World-wide.

When and Where---Tuesday at 11 am Room 350 Basic Science Building November 29, 2005.

Overview

Locally available software for use in viewing and discovering Drugs. This links to a web table which contains a brief description of licensed molecular modeling software that is available for researchers here at MUSC. Note in particular the Modeling and the Docking sections. The table has brief usage tips and on-line manuals.

Free One, Two molecular viewers described and used. See also this exercise for a sense of how to use viewers in a database mining manner.

Netware for Drugs. This link connects to PubChem, ChemFinder, KLOTHO and some additional web resources for drug and small molecule resources.

 

Introduction/Scope

Digital Chemistry

Binding Databases

Docking

Pharmacophores

Database Searching

Combinatorial Chemistry

 

A worked Example

We will work through the JACS COMFA and pharmacophore triplets tutorials and make a small combinatorial library within SYBYL.

 

Sample Questions/Data

Here some smiles strings to play with. Use PubChem or SYBYL to build 3D models and or find names and clinical use if any. 

CN(CC1=CN=C2C(=N1)C(=NC(=N2)N)N)C3=CC=C(C=C3)C(=O)NC(CCC(=O)O)C(=O)O


CCCc1c2c(c(=O)[nH]c(n2)c3cc(ccc3OCC)S(=O)(=O)N4CCN(CC4)C)n(n1)C


CCCC1=NN(C2=C1N=C(N=C2O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C

CC1=C2C(C(=O)C3C(CC4C(C3C(C(C2(C)C)(CC1OC(=O)C(C(C5=CC=CC=C5)NCC6=CC=CC=
C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)OC(=O)C

C1CCN(CC1)C2=NC(=N)N(C(=C2)N)O

CC(C(=O)C1=CC(=CC=C1)Cl)NC(C)(C)C.Cl

CS(=O)(=O)C1=CC=C(C=C1)C2=C(C(=O)OC2)C3=CC=CC=C3


CC1=CN=C(C(=C1OC)C)CS(=O)C2=NC3=C([N-]2)C=CC(=C3)OC.CC1=CN=C(C(=C1OC)C)CS(=O)C2=NC3=C([N-]2)C=CC(=C3)OC.O.O.O.[Mg+2]



CCSC1=CC2=C(C=C1)SC3=CC=CC=C3N2CCCN4CCN(CC4)C

CC1=C[C@@H]2[C@H](CC[C@]3([C@H]2CC[C@@]3(C(=O)C)OC(=O)C)C)[C@@]4(C1=CC(=O)CC4)C


C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO)O)O


C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O


C1=C(OC(=C1)[N+](=O)[O-])C=NO

CC1=C(C(CCC1)(C)C)CC[C@H](C)CCC[C@H](C)CCO

CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3

CN1CCN(CC1)C(=O)O[C@H]2C3=NC=CN=C3C(=O)N2C4=NC=C(C=C4)Cl

C1=CN=C2C(=N1)CN([C@]2OC(=O)N3CCNCC3)C4=NC=C(C=C4)Cl.CC=CC=C

CCC(CC)O[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)N)C(=O)O

CC(C)(C)C#CC=CCN(C)CC1=CC=CC2=CC=CC=C21

CC1=CC(=O)N(C(=C1)C2CCCCC2)O

CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NNC(=O)N)NC(=O)C(COC(C)(C)C)NC(=O)C(CC2=CC=C(C=C2)O)NC(=O)C(CO)NC(=O)C(CC3=CNC4=CC=CC=C43)NC(=O)C(CC5=CN=CN5)NC(=O)C6CCC(=O)N6

CC1C(C(CC(O1)O[C@H]2C[C@@](CC3=C(C4=C(C(=C23)O)C(=O)C5=CC=CC=C5C4=O)O)(C(=O)C)O)N)O.Cl

CCCCCC(C=CC1C(CC2C1CC(=CCCCC(=O)O)O2)O)O

CC[C@@H](C)C(=O)O[C@H]1[C@@H]([C@H]2[C@@H](CN3C[C@H](CC[C@H]3[C@@]2(C)O)C)[C@H]4[C@@]1([C@@H]5[C@@H]([C@@H]([C@H]6[C@]7(C5(C4)O[C@@]6([C@H](CC7)OC(=O)[C@](C)(CC)O)O)C)OC(=O)C)OC(=O)C)O)O

CCC(C)C(=O)OC1C(C2C(CN3CC(CCC3C2(C)O)C)C4C1(C5C(C(C6C7(C5(C4)OC6(C(CC7)OC(=O)C(C)(CC)O)O)C)OC(=O)C)OC(=O)C)O)O

CN1CC[C@@]23C=C[C@@H](C[C@@H]2OC4=C(C=CC(=C34)C1)OC)O

CC(C)(C)[C@]1(CCN2C[C@@H]3C4=CC=CC=C4CCC5=C3C(=CC=C5)[C@H]2C1)O

CN1CCCCC1CCN2C3=CC=CC=C3SC4=C2C=C(C=C4)SC.Cl

CC(C1=CC2=C(C=C1)C=C(C=C2)OC)C(=O)[O-].[Na+]

CC(=O)OC1CC2CCC3C(C2(CC1N4CCCCC4)C)CCC5(C3CC(C5OC(=O)C)[N+]6(CCCCC6)C)C.
[Br-]


CC1(C(N2C(S1)C(C2=O)NC(=O)C(C3=CC=C(C=C3)O)N)C(=O)O)C

CC12CCC3C(C1CCC2O)CCC4=C3C=CC(=C4)O

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Created by ESH 11-16-2005; updated 11-16-2005 11:30

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