Editing Ramachandran plot (section)

==More recent updates==
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined ([[myoglobin]], in 1960<ref>{{cite journal |pages=422–427 |year=1960 |last1=Kendrew |first1=J.C. |last2=Dickerson |first2=R.E. |last3=Strandberg |first3=B.E. |last4=Hart |first4=R.G. |last5=Davies |first5=D.R. |last6=Phillips |first6=D.C. |last7=Shore |first7=V.C. |title=Structure of myoglobin: a three-dimensional Fourier synthesis at 2Å resolution |journal=Nature |volume=185 |doi=10.1038/185422a0 |issue=4711 |pmid=18990802|bibcode=1960Natur.185..422K |s2cid=4167651 }}</ref>), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray [[crystallography]] and deposited in the [[Protein Data Bank|Protein Data Bank (PDB)]]. Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris ''et al.'' 1992;<ref name="ProCheck">{{cite journal |pages=345–64 |doi=10.1002/prot.340120407 |title=Stereochemical quality of protein structure coordinates |year=1992 |last1=Morris |first1=A.L. |last2=MacArthur |first2=M.W. |last3=Hutchinson |first3=E G. |last4=Thornton |first4=J.M. |journal=Proteins: Structure, Function, and Genetics |volume=12 |issue=4 |pmid=1579569|s2cid=940786 }}</ref> [[Gerard Kleywegt|Kleywegt]] & Jones 1996;<ref>{{cite journal |pmid=8994966 |year=1996 |last1=Kleywegt |first1=G.J. |last2=Jones |first2=T.A. |title=Phi/psi-chology: Ramachandran revisited |volume=4 |issue=12 |pages=1395–400 |journal=Structure |doi=10.1016/S0969-2126(96)00147-5|doi-access=free }}</ref> Hooft ''et al.'' 1997;<ref>{{cite journal|last1=Hooft|first1=R.W.W.|last2=Sander|first2=C.|last3=Vriend|first3=G.|title=Objectively judging the quality of a protein structure from a Ramachandran plot|journal=Comput Appl Biosci|year=1997|volume=13|issue=4|pages=425–430|doi=10.1093/bioinformatics/13.4.425|pmid=9283757|doi-access=free}}</ref> Hovmöller ''et al.'' 2002;<ref>{{cite journal |pmid=11976487 |year=2002 |last1=Hovmöller |first1=S. |last2=Zhou |first2=T. |last3=Ohlson |first3=T. |title=Conformations of amino acids in proteins |volume=58 |issue=Pt 5 |pages=768–76 |journal=Acta Crystallographica D |url=http://scripts.iucr.org/cgi-bin/paper?S0907444902003359 |doi=10.1107/S0907444902003359|url-access=subscription }}</ref> Lovell ''et al.'' 2003;<ref name="penultLib">{{cite journal |pages=437–50 |doi=10.1002/prot.10286 |title=Structure validation by Cα geometry: ϕ,ψ and Cβ deviation |year=2003 |last1=Lovell |first1=S.C. |last2=Davis |first2=I.W. |last3=Arendall |first3=W.B. |last4=De Bakker |first4=P.I.W. |last5=Word |first5=J.M. |last6=Prisant |first6=M.G. |last7=Richardson |first7=J.S. |last8=Richardson |first8=D.C. |journal=Proteins: Structure, Function, and Genetics |volume=50 |issue=3 |pmid=12557186|s2cid=8358424 }}</ref> Anderson ''et al.'' 2005''.<ref name="pmid16021632">{{cite journal |vauthors=Anderson RJ, Weng Z, Campbell RK, Jiang X | title = Main-chain conformational tendencies of amino acids | journal = Proteins | volume = 60 | issue = 4 | pages = 679–89 | year = 2005 | pmid = 16021632 | doi=10.1002/prot.20530| s2cid = 17410997 }}</ref> Ting ''et al.'' 2010<ref name="ndrd">{{cite journal |pages=e1000763 |title=Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model |year=2010 |last1=Ting |first1=D. |last2=Wang |first2=G. |last3=Mitra |first3=R. |last4=Jordan |first4=M.I. |last5=Dunbrack |first5=R.L. |journal=PLOS Computational Biology |volume=6 |issue=4 |pmid=20442867 |doi=10.1371/journal.pcbi.1000763 |pmc=2861699|bibcode=2010PLSCB...6E0763T |doi-access=free }}</ref>).

The four figures below show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.<ref name="penultLib"/> The most common regions are labeled: α for [[Alpha helix|α helix]], Lα for left-handed helix, β for [[beta sheet|β-sheet]], and ppII for polyproline II. Such a clustering is alternatively described in the ABEGO system, where each letter stands for α (and 3<sub>10</sub>) helix, right-handed β sheets (and extended structures), left-handed helixes, left-handed sheets, and finally unplottable cis peptide bonds sometimes seen with proline; it has been used in the classification of motifs<ref>{{cite journal |last1=Wintjens |first1=René T. |last2=Rooman |first2=Marianne J. |last3=Wodak |first3=Shoshana J. |title=Automatic Classification and Analysis of αα-Turn Motifs in Proteins |journal=Journal of Molecular Biology |date=January 1996 |volume=255 |issue=1 |pages=235–253 |doi=10.1006/jmbi.1996.0020|pmid=8568871 }}</ref> and more recently for designing proteins.<ref>{{cite journal |last1=Lin |first1=Yu-Ru |last2=Koga |first2=Nobuyasu |last3=Tatsumi-Koga |first3=Rie |last4=Liu |first4=Gaohua |last5=Clouser |first5=Amanda F. |last6=Montelione |first6=Gaetano T. |last7=Baker |first7=David |title=Control over overall shape and size in de novo designed proteins |journal=Proceedings of the National Academy of Sciences |date=6 October 2015 |volume=112 |issue=40 |pages=E5478–E5485 |doi=10.1073/pnas.1509508112|pmc=4603489 |pmid=26396255|bibcode=2015PNAS..112E5478L |doi-access=free }}</ref>

While the Ramachandran plot has been a textbook resource for explaining the structural behavior of peptide bond, an exhaustive exploration of how a peptide behaves in every region of the Ramachandran plot was only recently published  (Mannige 2017<ref>{{cite journal|last1=Mannige|first1=Ranjan|title=An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (''h'')|journal=PeerJ|date=16 May 2017|volume=5|page=e3327|doi=10.7717/peerj.3327|pmc=5436576|pmid=28533975 |doi-access=free }}</ref>).

The [[Molecular Biophysics]] Unit at Indian Institute of Science celebrated 50 years of Ramachandran Map<ref>{{cite web|title=50th Anniversary of Ramachandran Plots|url=http://sandwalk.blogspot.in/2013/01/50th-anniversary-of-ramachandran-plots.html|publisher=Professor [[Laurence A. Moran]]|accessdate=17 January 2013}}</ref> by organizing International Conference on Biomolecular Forms and Functions from 8–11 January 2013.<ref>{{cite web|title=ICBFF-2013|url=http://icbff2013.com/|publisher=MBU, IISc, Bangalore|accessdate=28 January 2013|archive-url=https://web.archive.org/web/20130115045506/http://icbff2013.com/|archive-date=15 January 2013|url-status=dead|df=dmy-all}}</ref>