Cyrus Chothia

Chothia was educated at Alleyn's School,{{cite web|archiveurl=https://web.archive.org/web/20150323230600/http://www.alleyns.org.uk/page.aspx?id=1406|archivedate=23 March 2015|url=http://www.alleyns.org.uk/page.aspx?id=1406|publisher=Alleyn's School|title=Dan David Prize Awarded to Dr Cyrus Chothia}} then went to study at Durham University graduating with a Bachelor of Science degree in 1965. Chothia then completed a Master of Science degree at Birkbeck College in 1967 and a PhD from University College London{{cite thesis |degree=PhD |first=Cyrus|last=Chothia |title=The crystal structures of some molecules active at cholinergic nerve receptors |publisher=University College London |year=1973 |id={{ProQuest|301370414}} |oclc=926297115 }} under the supervision of {{ill|Peter Pauling|qid=Q61761658|reasonator=1}},{{Cite journal

| last1 = Chothia | first1 = C.

| last2 = Pauling | first2 = P.

| title = On the conformations of hallucinogenic molecules and their correlation

| journal = Proceedings of the National Academy of Sciences of the United States of America

| volume = 63

| issue = 4

| pages = 1063–1070

| year = 1969

| pmid = 4311249

| pmc = 223427

| doi=10.1073/pnas.63.4.1063

|bibcode = 1969PNAS...63.1063C | doi-access = free

}} the son of Linus Pauling.

After his PhD Chothia worked in the Laboratory of Molecular Biology (LMB) for three years. He then worked with Michael Levitt{{cite web|archiveurl=https://web.archive.org/web/20150227104343/http://academictree.org/chemistry/peopleinfo.php?pid=72249|url=http://academictree.org/chemistry/peopleinfo.php?pid=72249|title=Cyrus H. Chothia, Chemistry Tree|archivedate=27 February 2015}} at the Weizmann Institute of Science{{Cite journal

| last1 = Chothia | first1 = C.

| last2 = Levitt | first2 = M.

| last3 = Richardson | first3 = D.

| title = Structure of proteins: Packing of alpha-helices and pleated sheets

| journal = Proceedings of the National Academy of Sciences of the United States of America

| volume = 74

| issue = 10

| pages = 4130–4134

| year = 1977

| pmid = 270659

| pmc = 431889

| doi=10.1073/pnas.74.10.4130

|bibcode = 1977PNAS...74.4130C | doi-access = free

}}{{Cite journal

| last1 = Levitt | first1 = M.

| authorlink1 = Michael Levitt (biophysicist)

| last2 = Chothia | first2 = C.

| authorlink2 = Cyrus Chothia

| title = Structural patterns in globular proteins

| journal = Nature

| volume = 261

| issue = 5561

| pages = 552–558

| year = 1976

| pmid = 934293

|bibcode = 1976Natur.261..552L |doi = 10.1038/261552a0 | s2cid = 4154884

}} followed by two years with Joel Janin at the Institut Pasteur in Paris.{{Cite journal

| last1 = Sweet | first1 = R.

| last2 = Wright | first2 = H.

| last3 = Janin | first3 = J.

| last4 = Chothia | first4 = C.

| last5 = Blow | first5 = D.

| title = Crystal structure of the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6-A resolution

| journal = Biochemistry

| volume = 13

| issue = 20

| pages = 4212–4228

| year = 1974

| pmid = 4472048 | doi=10.1021/bi00717a024

}}

In 1976 Chothia returned to England to work at University College London and the LMB. With Arthur Lesk{{Cite journal

| last1 = Lesk | first1 = A.

| last2 = Chothia | first2 = C.

| title = How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins

| journal = Journal of Molecular Biology

| volume = 136

| issue = 3

| pages = 225–270

| year = 1980

| pmid = 7373651

| doi=10.1016/0022-2836(80)90373-3

}}{{Cite journal

| last1 = Lesk | first1 = A.

| last2 = Chothia | first2 = C.

| doi = 10.1016/S0006-3495(80)84914-9

| title = Solvent accessibility, protein surfaces, and protein folding

| journal = Biophysical Journal

| volume = 32

| issue = 1

| pages = 35–47

| year = 1980

| pmid = 7248454

| pmc =1327253

|bibcode = 1980BpJ....32...35L }} he showed that proteins adapt to mutations by changes in structure.

In 1992 he proposed that most proteins are built of domains that come from a small number of families.{{Cite journal | doi = 10.1038/357543a0| title = One thousand families for the molecular biologist| journal = Nature| volume = 357| issue = 6379| pages = 543–4| year = 1992| last1 = Chothia | first1 = Cyrus | pmid=1608464|bibcode = 1992Natur.357..543C | s2cid = 4355476| doi-access = free}} He collaborated with Alexey Murzin, Steven Brenner and Tim Hubbard to create the Structural Classification of Proteins database (SCOP),{{Cite journal

| last1 = Hubbard | first1 = T. | authorlink1 = Tim Hubbard

| last2 = Murzin | first2 = A.

| last3 = Brenner | first3 = S. | authorlink3 = Steven E. Brenner

| last4 = Chothia | first4 = C. | authorlink4 = Cyrus Chothia

| title = SCOP: A structural classification of proteins database

| journal = Nucleic Acids Research

| volume = 25

| issue = 1

| pages = 236–239

| year = 1997

| pmid = 9016544

| pmc = 146380 | doi=10.1093/nar/25.1.236

}}{{cite web|archiveurl=https://web.archive.org/web/20141015061418/http://gtr.rcuk.ac.uk/person/63EF1EB9-4FB1-4759-8592-FD68CDBD168D|archivedate=15 October 2014|url=http://gtr.rcuk.ac.uk/person/63EF1EB9-4FB1-4759-8592-FD68CDBD168D|title=UK government grants awarded to Cyrus Chothia|publisher=Research Councils UK}} a periodic table for all known protein structures. With Julian Gough he created the Superfamily database{{Cite journal

| last1 = Gough | first1 = J.

| authorlink1 = Julian Gough (scientist)

| last2 = Chothia | first2 = C.

| authorlink2 = Cyrus Chothia

| title = SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

| journal = Nucleic Acids Research

| volume = 30

| issue = 1

| pages = 268–272

| year = 2002

| pmid = 11752312

| pmc = 99153

| doi=10.1093/nar/30.1.268

}} which uses Hidden Markov models to identify protein sequences that are related to those of known structures.

During his career, Chothia supervised 19 successful PhD students to completion{{cite web|archiveurl=https://web.archive.org/web/20150715093933/https://twitter.com/Alexbateman1/status/620860414675537920|archivedate=15 July 2015|url=https://twitter.com/Alexbateman1/status/620860414675537920|title=Cyrus Chothia's academic family tree|publisher=twitter|author=Alex Bateman|year=2015|url-status=dead|df=dmy-all}} including Alex Bateman, Steven E. Brenner, Mark Bender Gerstein, Julian Gough, Sarah Teichmann, Bissan Al-Lazikani,{{cite thesis|degree=PhD|first=Bissan|last=Al-Lazikani|title=Canonical structures of immunoglobulins and T cell receptors|publisher=University of Cambridge|year=1999|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624098}}{{cite web|archiveurl=https://web.archive.org/web/20150305201555/http://www.icr.ac.uk/our-research/researchers-and-teams/dr-bissan-al-lazikani|archivedate=5 March 2015|title=Dr Bissan Al-Lazikani Team leader|publisher=The Institute of Cancer Research|url=http://www.icr.ac.uk/our-research/researchers-and-teams/dr-bissan-al-lazikani}}{{Cite journal

| pmid = 10656805

| year = 2000

| last1 = Al-Lazikani

| first1 = B

| title = Canonical structures for the hypervariable regions of T cell alphabeta receptors

| journal = Journal of Molecular Biology

| volume = 295

| issue = 4

| pages = 979–95

| last2 = Lesk

| first2 = A. M.

| last3 = Chothia

| first3 = C

| doi = 10.1006/jmbi.1999.3358

}} Goga Apic,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Evolution of multidomain proteins in genomes|first=Gordana|last=Apic|year=2003|url=http://idiscover.lib.cam.ac.uk/primo-explore/fulldisplay?docid=44CAM_ALMA21433441040003606&context=L&vid=44CAM_PROD&search_scope=SCOP_CAM_ALL&tab=cam_lib_coll&lang=en_US|id={{EThOS|uk.bl.ethos.619919}}|website=lib.cam.ac.uk|oclc=894594841}} Samantha Barré{{citation needed|date=February 2017}}{{cite journal|last1=Barré|first1=Samantha|last2=Greenberg|first2=Andrew S.|last3=Flajnik|first3=Martin F.|last4=Chothia|first4=Cyrus|title=Structural conservation of hypervariable regions in immunoglobulins evolution|journal=Nature Structural Biology|volume=1|issue=12|year=1994|pages=915–920 |doi=10.1038/nsb1294-915|pmid=7773781|s2cid=39728494}} Matthew Bashton,{{cite thesis|degree=PhD|first=Matthew|last=Bashton|title=Functional analysis of domain combinations|publisher=University of Cambridge|year=2004|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616149}}{{cite web|url=http://www.ncl.ac.uk/biomedicine/contact/team/profile/matthew.bashton|archiveurl=https://web.archive.org/web/20150305201647/http://www.ncl.ac.uk/biomedicine/contact/team/profile/matthew.bashton|archivedate=5 March 2015|title=Dr Matthew Bashton: Research Associate: INSTINCT project}}{{Cite journal

| pmid = 11812158

| year = 2002

| last1 = Bashton

| first1 = M

| title = The geometry of domain combination in proteins

| journal = Journal of Molecular Biology

| volume = 315

| issue = 4

| pages = 927–39

| last2 = Chothia

| first2 = C

| doi = 10.1006/jmbi.2001.5288

}}{{Cite journal

| pmid = 17223535

| year = 2007

| last1 = Bashton

| first1 = M

| title = The generation of new protein functions by the combination of domains

| journal = Structure

| volume = 15

| issue = 1

| pages = 85–99

| last2 = Chothia

| first2 = C

| doi = 10.1016/j.str.2006.11.009

| doi-access = free

}} Dan Bolser,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=The surfaces involved in the formation of protein complexes|first= Daniel Murray|last=Bolser|year=2007|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612938}} Michael Bremang,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=The mouse protein repertoire : studies on alternative splicing, function and quality|first= Michael Anthony|last=Bremang|year=2012|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610626}} Bernard de Bono,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Immunoglobulin superfamily proteins in human and mouse|first= Bernard|last=de Bono|year=2004|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598443}}{{cite journal|last1=de Bono|first1=B.|title=Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes|journal=Nucleic Acids Research|volume=31|issue=21|year=2003|pages=6096–6103 |doi=10.1093/nar/gkg828|pmid=14576296|pmc=275470}} Emma Ganley (née Hill),{{cite thesis|degree=PhD|first=Emma Elizabeth|last=Hill|title=Evolution of protein families: genome sequences and three dimensional structures|publisher=University of Cambridge|year=2002|url=http://ulmss-newton.lib.cam.ac.uk/vwebv/holdingsInfo?bibId=23724}}{{cite web|archiveurl=https://web.archive.org/web/20060713231419/http://compbio.berkeley.edu/people/emma/aboutme.html|archivedate=13 July 2006|title=Emma Hill's Homepage|publisher=University of California, Berkeley|url=http://compbio.berkeley.edu/people/emma/aboutme.html}}{{cite web|archiveurl=https://web.archive.org/web/20150424211743/https://www.plos.org/staff/emma-ganley/|archivedate=24 April 2015|url=https://www.plos.org/staff/emma-ganley/|publisher=PLOS|title=Emma Ganley (née Hill) PLOS staff}} Martin Madera,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Hidden Markov models for detection of remote homology|first= Martin|last=Madera|year=2005|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615112}}{{cite journal|last1=Madera|first1=M.|title=The SUPERFAMILY database in 2004: additions and improvements|journal=Nucleic Acids Research|volume=32|issue=90001|year=2004|pages=235D–239 |doi=10.1093/nar/gkh117|pmid=14681402|pmc=308851}} Siarhei Maslau,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Formation of the small molecule metabolism of Escherichia coli|first= Siarhei|last=Maslau|year=2007|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613391}} Susan Miller,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Computer display and manufacture of 3-D models|first= G. S. P.|last=Miller|year=1987|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235044|oclc=59769936}}{{cite journal|last1=Miller|first1=Susan|last2=Janin|first2=Joël|last3=Lesk|first3=Arthur M.|last4=Chothia|first4=Cyrus|title=Interior and surface of monomeric proteins|journal=Journal of Molecular Biology|volume=196|issue=3|year=1987|pages=641–656 |doi=10.1016/0022-2836(87)90038-6|pmid=3681970}}{{cite journal|last1=Miller|first1=Susan|last2=Lesk|first2=Arthur M.|last3=Janin|first3=Joël|last4=Chothia|first4=Cyrus|title=The accessible surface area and stability of oligomeric proteins|journal=Nature|volume=328|issue=6133|year=1987|pages=834–836 |doi=10.1038/328834a0|pmid=3627230|bibcode = 1987Natur.328..834M |s2cid=4349684}} Jong Park (aka Jong Bhak),{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Genome sequence analysis and methods|first= Jong Hwa|last=Park|year=1997|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627329}}{{GoogleScholar|id=ZUBVdMAAAAAJ}}{{cite web|archiveurl=https://web.archive.org/web/20141220015716/http://jongbhak.com/index.php/Main_Page|archivedate=20 December 2014|url=http://jongbhak.com/index.php/Main_Page|title=Jong Bhak's home page: An entrepreneur and a scientist|publisher=jongbhak.com}} Rajkumar Sasidharan,{{cite thesis|degree=PhD|publisher=University of Cambridge|title=Protein evolution : the selection of acceptable mutations|first= Rajkumar|last=Sasidharan|year=2004|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616044}}{{cite journal|last1=Sasidharan|first1=R.|last2=Chothia|first2=C.|title=The selection of acceptable protein mutations|journal=Proceedings of the National Academy of Sciences|volume=104|issue=24|year=2007|pages=10080–10085 |doi=10.1073/pnas.0703737104|pmid=17540730|bibcode = 2007PNAS..10410080S |pmc=1891269|doi-access=free}} and Christine Vogel.{{cite thesis|degree=PhD|publisher=University of Cambridge|title=A domain perspective on the evolution of the protein repertoire|first= Christine|last=Vogel|year=2004|url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616272}}{{cite journal|last1=Vogel|first1=Christine|last2=Chothia|first2=Cyrus|title=Protein Family Expansions and Biological Complexity|journal=PLOS Computational Biology|volume=2|issue=5|year=2006|pages=e48 |doi=10.1371/journal.pcbi.0020048|bibcode = 2006PLSCB...2...48V|pmid=16733546|pmc=1464810 |doi-access=free }} {{open access}}

Chothia was elected a Fellow of the Royal Society (FRS) in 2000. His certificate of election and candidature reads: {{centred pull quote|Dr Chothia has shown how the amino sequences of proteins determine their structure, function and evolution. From an analysis of their structural regularities, he has developed a classification of protein structures that is now in general use. His picture of protein evolution suggests how proteins diverge and gain new functions. He has helped us to understand how their apparently limited set of slightly different structures allow immunoglobin to recognise an almost limitless variety of different antigens.{{cite web|url=https://collections.royalsociety.org/DServe.exe?dsqIni=Dserve.ini&dsqApp=Archive&dsqDb=Catalog&dsqCmd=show.tcl&dsqSearch=(RefNo==%27EC%2F2000%2F04%27)|title=EC/2000/04: Chothia, Cyrus|publisher=Royal Society|accessdate=18 November 2013|location=London|archiveurl=https://web.archive.org/web/20220329174119/https://collections.royalsociety.org/DServe.exe?dsqIni=Dserve.ini&dsqApp=Archive&dsqDb=Catalog&dsqCmd=show.tcl&dsqSearch=(RefNo==%27EC%2F2000%2F04%27)|archivedate=29 March 2022|url-status=dead|df=dmy-all}}}}

In 2015, Chothia was elected a Fellow of the International Society for Computational Biology (ISCB){{cite journal | last1=Fogg | first1=C. N. | last2=Kovats | first2=D. E. | title=Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia | journal=Bioinformatics | volume=31 | issue=13 | pages=2238–9 | year=2015 | doi=10.1093/bioinformatics/btv218 | pmid= 26002905| doi-access=free }} and was awarded the ISCB Accomplishment by a Senior Scientist Award in honour of his work in using computational methods to understand protein structure.{{cite web|title=Meet the ISCB Fellows Class of 2015|url=http://www.iscb.org/iscb-news-items/2392-2015feb20-meet-the-iscb-fellows-class-of-2015|accessdate=15 February 2015|archiveurl=https://web.archive.org/web/20150220233807/http://www.iscb.org/iscb-news-items/2392-2015feb20-meet-the-iscb-fellows-class-of-2015|archivedate=20 February 2015}}

Alongside David Haussler and Michael Waterman, Chothia was awarded the 2015 Dan David Prize for his contributions to the field of bioinformatics.

{{Scholia}}

{{reflist|2}}

{{FRS 2000}}

{{ISCB Fellows}}

{{CC-notice|cc=by4|url= https://royalsociety.org/people/cyrus-chothia-11220/}}

{{Authority control}}

{{DEFAULTSORT:Chothia, Cyrus}}

Category:British bioinformaticians

Category:Fellows of the Royal Society

Category:Fellows of Wolfson College, Cambridge

Category:Place of birth missing

Category:Alumni of University College London

Category:Academics of University College London

Category:People educated at Alleyn's School

Category:1942 births

Category:2019 deaths

Category:Fellows of the International Society for Computational Biology

Category:Alumni of University College, Durham

Category:Academic staff of Weizmann Institute of Science

Category:Pasteur Institute

Category:British people of Parsi descent