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<meta name="keywords" content="Protein Domains and Macromolecular Structures, Aron Marchler-Bauer, group leader, Stephen H. Bryant, Steve Bryant, Senior Investigator Emeritus, Structure Group of the National Center for Biotechnology Information (NCBI) Computational Biology Branch (CBB), Molecular Modeling Database, MMDB, 3D Domains, Vector Alignment Search Tool, VAST, nrPDB, Cn3D structure viewing software, CBLAST, Entrez Protein related structure links, 3-D, 3D, three-dimensional structures, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, proteins, nucleic acids, DNA, RNA, ligands, Conserved Domain Database (CDD), CDART, SPARCLE, CD-Search, CDTree, mutliple sequence alignments, PubChem, BioSystems Database, Biological Systems, Biochemical Metabolic Pathways" />
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<TD class="DocTitleText" align="left"> Protein Domains and Macromolecular Structures</TD>
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<!-- ================== BOX1_RESEARCH_PROGRAMS ====================== -->
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Services</TD>
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<P class="indent10 NormalText">As part of the NCBI <SPAN class="TOCText2"><A HREF="/home/about/structure/">Information Engineering Branch</A></SPAN>, the Protein Classification and Structure Group provides an array of services in bioinformatics and computational approaches to protein classification, including:</P>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="InfoTech"></A><A HREF="index.shtml">Bioinformatics</A></TD>
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Development of "computer-friendly" databases for conserved domains (<A HREF="/cdd"><B>CDD</B></A>) and macromolecular structures (<A HREF="/structure"><B>MMDB</B></A>); development of retrieval software; and development of methods (e.g., <A HREF="/Structure/VAST/vast.shtml"><B>VAST</B></A>, <A HREF="cdd/cdd_help.shtml#RPSBWhat"><B>RPS-BLAST</B></A>, <A HREF="/Structure/lexington/lexington.cgi?cmd=rps"><B>CDART</B></A>, <A HREF="/sparcle"><B>SPARCLE</B></A>) to identify associations among the data as part of the broader NCBI effort to facilitate biological <A HREF="structure_discover.html"><B>discovery</B></A>.</TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="ProtClass"></A><A HREF="cdd/cdd.shtml">Protein Classification</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">The
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<A HREF="cdd/cdd_help.shtml#CDSource_NCBI_curated"><B>CDD curation project</B></A></SPAN> for <A HREF="cdd/cdd_help.shtml#CDWhat">conserved domains</A> provides insights into how patterns of residue conservation and divergence in a family relate to functional properties, and insights into <A HREF="cdd/cdd_help.shtml#NCBI_curated_domains">sequence/structure/function relationships</A>.<BR>
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A companion tool, <A HREF="/sparcle"><B>SPARCLE</B>, the <B>S</B>ubfamily <B>P</B>rotein <B>Arc</B>hitecture <B>L</B>abeling <B>E</B>ngine</A>, is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic <A HREF="lexington/docs/cdart_help.html#WhatIs">conserved domain architecture</A>. <!-- A domain architecture is defined as the sequential order of <A HREF="cdd/cdd_help.shtml#CDWhat">conserved domains</A> in a protein sequence. --> <I><A HREF="cdd/cdd.shtml">more...</A></I></TD>
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<TD colspan="4" class="WhiteCell MiniText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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 </TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="3Dvisual"></A><A HREF="icn3d/docs/icn3d_about.html">3D Visualization</A></TD>
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Visualization and analysis of <A HREF="MMDB/docs/mmdb_help.html#WhatIs">three-dimensional structures</A> with emphasis on interactive examination of <A HREF="MMDB/docs/mmdb_how_to_view_in_cn3d.html">sequence-structure relationships</A> and superposition of geometrically similar structures with the original <SPAN class="ThumbText"><A HREF="CN3D/cn3d.shtml"><B>Cn3D</B></A></SPAN> standalone software program, and the newer <A HREF="icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the web, without the need to install a separate application. <I><A HREF="icn3d/docs/icn3d_about.html">more...</A></I></TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="3Dcompare"></A><A HREF="VAST/vast.shtml">3D Structure Comparisons</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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Development of the <SPAN class="ThumbText"><A HREF="VAST/vast.shtml"><B>VAST</B></A></SPAN> algorithm and <SPAN class="ThumbText"><A HREF="VAST/vastsearch.html"><B>VAST Search</B></A></SPAN> tool to identify similar 3D structures based on geometric methods; application of the algorithm on all publicly available, experimentally resolved protein structures in order to identify structures that are similar in shape, regardless of their degree of sequence similarity. <I><A HREF="VAST/vast.shtml">more...</A></I></TD>
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 </TD>
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<A HREF="___">Research Area...</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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brief description that includes <SPAN class="ThumbText"><A HREF="____"><B>__resource_link___</B></A></SPAN></TD>
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<P class="indent10 NormalText">Previous work by the group, as part of the NCBI <SPAN class="TOCText2"><A HREF="/CBBresearch/">Computational Biology Branch (CBB)</A></SPAN>, included the services above as well as the following research areas:</P>
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<A NAME="InfoTech"></A><A HREF="index.shtml">Bioinformatics</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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In addition to the ongoing bioinformatics work above, previous work included development of "computer-friendly" databases small molecules and their biological properties (<A HREF="https://pubchem.ncbi.nlm.nih.gov/"><B>PubChem</B></A>) and biological systems (<A HREF="/biosystems/"><B>BioSystems</B></A>). As a result of growth in the small molecules resources, those resources have branched off into a parallel group (Chemistry) in the Information Engineering Branch and continue to be available.</TD>
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<A NAME="MolInteract"></A><!-- A HREF="ibis/ibis.cgi" --><A HREF="/pubmed/22102591">Biomolecular Interactions</A></TD>
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Analysis of interactions that have been observed across numerous experimentally determined 3D macromolecular structures in order to identify interaction sites, and to characterize and infer common types of interactions observed among homologous structures, particularly interactions between proteins and other biopolymers or chemicals (<SPAN class="ThumbText"><A HREF="/pubmed/22102591"><B>IBIS</B></A></SPAN>). <I><A HREF="/pubmed?cmd=search&term=22303436+22261719+22198293+22153503+22102591+21572178+21048085+20594344+20544079+20381499+19879880+19843613+19591200+19573245+19394310+19289044+19282967+18930732+18831050+17135201+18984618+15215404+10838572+17681537+19498078">more...</A></I></TD>
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<A NAME="Cheminformatics"></A><A HREF="https://pubchem.ncbi.nlm.nih.gov">Cheminformatics</A></TD>
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Development of algorithms to compute, compare, and analyze the structure and physicochemical and biological properties of chemicals in the <A HREF="https://pubchem.ncbi.nlm.nih.gov/"><B>PubChem</B></A> databases. As a result of growth in the small molecules resources, those resources have branched off into a parallel group (Chemistry) in the Information Engineering Branch and continue to be available. <I><A HREF="https://pubchem.ncbi.nlm.nih.gov/publications.html">more...</A></I></TD>
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<A NAME="Threading"></A><!-- A HREF="RESEARCH/threading.shtml" --><A HREF="//ftp.ncbi.nih.gov/pub/pkb">Threading</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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Development of algorithms for Protein Knowledge Base (<SPAN class="ThumbText"><A HREF="//ftp.ncbi.nih.gov/pub/pkb"><B>PKB</B></A></SPAN>), a suite of software programs (written in the Splus language) for the convenient study and analysis of biomolecular structure data, including programs for protein fold recognition ("threading"). <I><A HREF="/pubmed/2780541">more...</A></I></TD>
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<A HREF="___">Research Area...</A></TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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brief description that includes <SPAN class="ThumbText"><A HREF="____"><B>__resource_link___</B></A></SPAN></TD>
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<!-- ============== BOX2_PI_THUMBNAILS ================ -->
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<A NAME="___"></A>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Group Leader</TD>
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<A HREF="/pubmed/?term=Marchler-Bauer%20A%5BAuthor%5D&cauthor=true&cauthor_uid=31777944"><B>Aron Marchler-Bauer, Ph.D.</B></A><BR>
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<A HREF="/home/about/structure/">Information Engineering Branch</A><BR>
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<A HREF="/">National Center for Biotechnology Information (NCBI)</A><BR>
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<A HREF="https://www.nlm.nih.gov/">National Library of Medicine (NLM)</A><BR>
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<A HREF="https://www.nih.gov/">National Institutes of Health</A><BR>
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Contact:<BR>
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Dr. Aron Marchler-Bauer<BR>
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Bldg. 38A, Room 5S508, NCBI/NLM/NIH<BR>
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8600 Rockville Pike<BR>
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Bethesda, MD 20894<BR>
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Tel: 301-435-4919<BR>
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Fax: 301-480-9241 or 301-435-7793<BR>
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E-mail: <A HREF="mailto:bauer@ncbi.nlm.nih.gov">bauer@ncbi.nlm.nih.gov</A>
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<img SRC="IMG/spacer.gif" width="10" height="1" border="0">
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<IMG src="IMG/Aron.png" width="153" height="175" border="0" alt="photo of Dr. Aron Marchler-Bauer, Group Leader, Protein Classification and Structure, NCBI, from NLM Awards Ceremony, October 30, 2013">
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<TD class="Yellow1Cell TOCText" ALIGN="LEFT" VALIGN="TOP"><i>(left to right) Steve Bryant, Aron Marchler-Bauer, and Anna Panchenko</i></TD>
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<!-- ======= END_ARON_MARCHLER_BAUER_CONTACT_INFO ====== -->
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<!-- ======= BEGIN_STEVE_BRYANT_CONTACT_INFO ====== -->
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Senior Investigator, Emeritus</TD>
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<TD class="Yellow1Cell TOCText" ALIGN="LEFT" VALIGN="TOP"><b>Senior Investigator, Emeritus:</b></TD>
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<A HREF="/pubmed?cmd=search&term=bryant%20sh%5Bau%5D%20NOT%20%28Chloride%20Channels%5Bmh%5D%20OR%20Membrane%20Potentials%20%5Bmh%5D%20OR%20Electrophysiology%5Bmh%5D%20OR%20Ion%20Channels%5Bmh%5D%20OR%20Neural%20Conduction%5Bmh%5D%20OR%20Muscles%5Bmh%5D%20OR%20Drosophila%5Bmh%5D%20OR%20Goats%5Bmh%5D%20OR%20Pigeons%5Bmh%5D%20OR%20Colchicine%5Bmh%5D%20OR%20Mollusca%5Bmh%5D%29"><B>Stephen H. Bryant, Ph.D.</B></A><BR>
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Senior Investigator, Emeritus<BR>
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<A HREF="/CBBresearch/">Computational Biology Branch</A><BR>
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<A HREF="/">National Center for Biotechnology Information (NCBI)</A><BR>
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<A HREF="https://www.nlm.nih.gov/">National Library of Medicine (NLM)</A><BR>
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<A HREF="https://www.nih.gov/">National Institutes of Health</A><BR>
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E-mail: <A HREF="mailto:bryant@ncbi.nlm.nih.gov">bryant@ncbi.nlm.nih.gov</A>
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<IMG src="IMG/Bryant-2color_50.jpg" width="153" height="247" border="0" alt="photo of Dr. Stephen H. Bryant, Senior Investigator, NCBI, from PubChem project announcement in May-June 2004 NIH Catalyst //www.nih.gov/catalyst/2004/04.05.01/page1a.html">
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<P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P>
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<!-- ==================== VERTICAL_SPACER ======================= -->
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 31 January 2020</SPAN></TD>
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<!-- ##################### END_EDITABLE_CONTENT ##################### -->
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<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="/home/about/structure/">Information Engineering Branch</A> > <A HREF="/Structure/index.shtml">Protein Domains and Macromolecular Structures</A> > Services','other');</script>
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