Here my hot list of links to model 3D structures 
<P>
<ul>
 <li>  <a href="http://www.robetta.org/submit.jsp"> ROBETTA  server</a>
 <li>  <a href="http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html"> 3D-PSSM   server</a>
 <li>  <a href="http://www.sbg.bio.ic.ac.uk/~phyre/"> PHYRE   server</a>
 <li>  <a href="http://swift.cmbi.kun.nl/WIWWWI/makemodel.html"> WIWWWI server</a>
 <li>  <a href="http://www1.jcsg.org/scripts/prod/scwrl/serve.cgi ">SCWRL server </a>
 <li>  <a href="http://www.bmm.icnet.uk/servers/3djigsaw/">3D JIGSAW  server </a>
 <li>  <a href="http://swissmodel.expasy.org//SWISS-MODEL.html">SWISS MODEL  server </a>
 <li>  <a href="http://proline.bic.nus.edu.sg/sdpmod/modeling.html"> Small Disulphide-bonded Proteins Modeling server </a>
 <li>  <a href="http://alto.compbio.ucsf.edu/modweb-cgi/main.cgi">MOD-WEB   server </a>
 <li>  <a href="http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl"> FFAS03: Fold & Function Assignment System </a>
 <li>  <a href="http://swift.cmbi.ru.nl/servers/html/index.html"> Build model from template  </a>

</ul>

DNA-RNA Modeling

<ul>
 <li>  <a href="http://structure.usc.edu/make-na"> Make-NA </a>
 <li>  <a href="http://www.scripps.edu/mb/case/Biomer/"> BIOMER java </a>
 <li>  <a href="http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html"> 3DNA </a>
 <li>  <a href="http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html">  MFOLD </A>
 <li>  <a href="http://www.ibpc.fr/UPR9080/Curindex.html">  CURVES: DNA Analysis </A>
</ul>
ACCESIBLE AREA CALCULATION

<ul>
 <li>  <a href="http://redpoll.pharmacy.ualberta.ca/vadar/"> VADAR </a>
</ul>
EDUCATIONAL 
<ul>
<li> <a href="http://lcr.epfl.ch/page37304.html"> Interactive Course in Crystallography </a>
</ul>