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1 <HTML>
2 <HEAD>
3 <TITLE>SCOL: The Structural Classification of Ligands</TITLE>
4 <HEAD>
5 <BODY>
6
7 <TABLE WIDTH='100%'><TR>
8 <TD>
9 <H1>SCOL :</H1>
10 <H2>The Structural Classification of Ligands</H2>
11 </TD>
12 <TD>
13 <A HREF='logo.html'>
14 <IMG
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16 SRC='Image/1kar-best-pals-small.gif'
17 ALT='Young proteins in love'
18 >
19 </A>
20 </TD>
21 </TR></TABLE>
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23
24 <HR WIDTH='80%'>
25
26 <BLOCKQUOTE>
27
28 "Students look at the support, honours, prizes, and rewards lavished on X-ray crystallographers and molecular geneticists and they want to be there. By working within these fashionable fields, scientific creativity, adapted to a flourishing technology, can still exist and be recognised. <I>Outside</I> of these fashionable directions, however, although survival is possible, recognition is extremely difficult."
29 <CREDIT><A HREF='http://en.wikipedia.org/wiki/Robert_G._Shulman'>Robert G. Shulman</A></CREDIT>
30
31 </BLOCKQUOTE>
32
33 <HR WIDTH='80%'>
34
35 <H3>Project Overview</H3>
36
37 <H4>Objectives</H4>
38
39 <P>The objective of the SCOL project is to produce a global <A HREF='http://en.wikipedia.org/wiki/Hierarchical_Clustering'>hierarchical clustering</A> of all the available <A HREF='http://en.wikipedia.org/wiki/Small_Molecule'>small molecules</A> and <A HREF='http://en.wikipedia.org/wiki/Protein_Ligand'>protein ligands</A> using measures of structural and chemical 'similarity' between molecules.
40
41 At a broad level, this hierarchical classification should reflect biological and chemical intuitions about the major classes of molecule and their broad physical and chemical characteristics.
42
43 At a more detailed level of classification, structurally and chemically similar molecules should be grouped together.
44
45 This classification system should prove useful for diverse studies, from the gross assessment of metabolic evolution to <A HREF='http://en.wikipedia.org/wiki/Ligand_Binding'>ligand binding</A> studies.
46
47 The ultimate aim is to assist in the process of <A HREF='http://en.wikipedia.org/wiki/Drug_Discovery'>drug discovery</A> and <A HREF='http://en.wikipedia.org/wiki/Lead_Compound'>lead compound</A> identification.
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49 A distinct sub project of SCOL is the derivation of a set of 'representative' or 'non-redundant' compounds for input into more detailed structural and functional studies.
50
51 <HR>
52
53 <H4>Goals / Independent Sub-Tasks</H4>
54
55 <P>The overall objectives of SCOL can be broken down into several different but overlapping activities.
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57 Some tasks are purely technical, while others require substantial background research.
58
59 Other tasks will require the investigation and development of novel areas of research.
60
61 Many of the preliminary subtasks have already been completed by various different groups, and may or may not be directly applicable to the development of SCOL.
62 Some or all of these tasks may reflect my ignorance and you are invited to fix this with out delay!
63
64 No doubt you can think of many other interesting and/or practical sub tasks, which you can add by joining the project!
65
66 <UL>
67
68 <LH>Task List:</LH>
69
70 <P>
71 <LI>Obtain a comprehensive database of small molecule structures.
72 <LI>Implement libraries of chemical / physiochemical properties of small molecules and atoms.
73 <LI>Assess the state of predictive software for the automatic analysis of small molecules. <i>e.g. predicting hydrophobicity, pK, etc.</i>
74 <LI>Implement visualisation interface to various chemical structures and physical properties.
75 <LI>Implement similarity measures between small molecules based on combinations of structural, physical and chemical properties.
76 <LI>Develop clustering strategies over the similarly measures (similarity matrices) in order to assess the most useful notions of 'similarity' between small molecules and at what level of detail these measures are most appropriate.
77 <LI>Assess the best 'ontology' for the classification. e.g. is a DAG more appropriate than a strict hierarchy?
78 <LI>Develop visualisation interface to hierarchical clusterings.
79 <LI>Assess the overlap between biological notions of 'good clusters' versus the purely algorithmic 'goodness of clusters' given the different similarity measures and clustering algorithms used.
80 <LI>Investigate issues of modularity in small molecule structure, using both information from the perspective of cluster splitting and detailed knowledge of modular assembly derived from bio-synthesis pathways.
81 <LI>Investigate potential 'homologous' relationships between structurally similar ligands with biological analysis of the ligand.
82 <LI>Investigate 'biological' measures of similarity derived from the evolution of ligand binding proteins, and assess the overlap with SCOL.
83 <LI>Investigate the potential predictive power of SCOL.
84 <LI>Develop new potential drugs using SCOL.
85
86 </UL>
87
88 <HR>
89
90 <H4>Related Projects / Resources</H4>
91 <P>This list is by no means exhaustive. If you would like to be included (or removed) or if you have a link you recomend, please contact me.
92
93 <UL>
94
95 <LH>Links List:</LH>
96
97 <P>
98 <LI>Existing work on ligand classification.
99 <LI><A HREF='http://www.genome.ad.jp/kegg/catalog/compounds.html'>A partial classification of the COMPOUND database</A>
100 <LI><A HREF='http://science.ntu.ac.uk/projects/Organometallics/James/topics/intro/E_DONOR.HTM'>Ligand Classification</A>
101 <LI><A HREF='http://www.google.com/search?q=ligand+classification'>Google</A>
102
103 <P>
104 <LI>Compound databases
105 <LI><A HREF='http://www-mitchell.ch.cam.ac.uk/databases.html'>Protein Ligand Databases</A>
106 <LI><A HREF='http://www.expasy.org/enzyme/'>ENZYME</A>
107 <LI><A HREF='http://www.genome.ad.jp/dbget/ligand.html'>LIGAND</A>
108 <LI><A HREF='http://www.ebi.ac.uk/msd-srv/chempdb/cgi-bin/cgi.pl'>MSD Ligand Chemistry</A>
109 <LI><A HREF='http://www.ccdc.cam.ac.uk/csd/'>Cambridge Structural Database</A>
110 <LI><A HREF='http://www.google.com/search?q=compound+databases'>Google</A>
111
112
113 <P>
114 <LI>Compound prediction software
115 <LI><A HREF='http://www2.chemie.uni-erlangen.de/software/corina/index.html'>CORINA</A>
116 <LI>MOLEGO
117 <LI>CHEM-X
118 <LI>COBRA
119 <LI>ALCOGEN
120 <LI>CONCORD
121 <LI>CONVERTER
122 <LI><A HREF='http://www.google.com/search?q=compound+prediction+software'>Google</A>
123
124 <P>
125 <LI>Molecular visualisation packages
126 <LI><A HREF='http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html'>LIGPLOT</A>
127 <LI><A HREF='http://www.bmsc.washington.edu/raster3d/raster3d.html'>Raster3D</A>
128 <LI><A HREF='http://jmol.sourceforge.net/'>Jmol</A>
129 <LI><A HREF='http://www.umass.edu/microbio/rasmol/'>Protein Explorer</A>
130 <LI><A HREF='http://www.openrasmol.org/'>RasMol</A>
131 <LI><A HREF='http://users.unimi.it/~ddl/vega/index.htm'>VEGA</A>
132 <LI><A HREF='http://www.google.com/search?q=molecular+visualization+packages'>Google</A>
133
134 <P>
135 <LI>Protein ligand interactions
136 <LI><A HREF='http://relibase.ebi.ac.uk/reli-cgi/rll?/reli-cgi/general_layout.pl+home'>Relibase</A>
137 <LI><A HREF='http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html'>LIGPLOT</A>
138 <LI><A HREF='http://bip.weizmann.ac.il/oca-bin/lpccsu'>LPC</A>
139 <LI><A HREF='http://bioinfo.weizmann.ac.il/ligprot/'>LIGPROT</A>
140 <LI><A HREF='http://www.biochem.ucl.ac.uk/bsm/pdbsum/'>PDBsum</A>
141 <LI><A HREF='http://www.google.com/search?q=protein+ligand+interactions'>Google</A>
142
143 <P>
144 <LI>Useful links
145 <LI><A HREF='http://www.ch.ic.ac.uk/chemime/'>Chemical MIME</A>
146 <LI><A HREF='http://www2.chemie.uni-erlangen.de/software/cactvs/index.html'>CACTVS</A>
147 <LI><A HREF='http://www.google.com/'>Google</A>
148
149
150 </UL>
151
152 <HR>
153
154 <H4>Project Licence</H4>
155 <P>This project is not 'open' in the strict sense. To work on SCOL you must first agree to the <A HREF='http://biomatics.kaist.ac.kr/Research/Biolicense/'>BiO Licence</A>, a summary of which is given <A HREF='licence.html'>hear</A>.
156
157 <HR>
158
159 <A HREF='mailto:dmb@bioinformatics.org?subject=CD-HIT Project Web Page'><I>Comments and suggestions</I></A>
160
161 <HR WIDTH='80%'>
162
163 <BLOCKQUOTE>"However, individuals choosing such an unfashionable direction must have the passionate vision enabling them to bear considerable neglect and be able to settle for less recognition. Young biochemists have low morale not because their chances to flourish are not described clearly and honestly by caring elders, but because the opportunities available require that their passions be subordinated to fashionable directions that emphasis technical activities at the expense of biological goals."
164 <CREDIT><A HREF='http://www.fasebj.org/cgi/content/full/12/3/255'>Hard Days in the Trenches</A>, <A HREF='http://en.wikipedia.org/wiki/Robert_G._Shulman'>Robert G. Shulman</A></CREDIT>
165
166 </BLOCKQUOTE>
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172 </HTML>