mandatory to put some order in such a vast wealth of structural knowledge 4. Nucleic acids and proteins in one and more dimensions - second part
Learning from Biology Taxonomy (from Ancient Greek: τάξις taxis, "arrangement," and -νομία -nomia, "method") is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Organisms are grouped together into taxa (singular: taxon) and given a taxonomic rank; groups of a given rank can be aggregated to form a super group of higher rank and thus create a taxonomic hierarchy. 4. Nucleic acids and proteins in one and more dimensions - second part
Learning from Biology 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy red: mainly α green: mainly β yellow: αβ blue: low content of secondary structures 4. Nucleic acids and proteins in one and more dimensions - second part
protein structure taxonomy most of different protein folds have been already found? from http://www.proteinstructures.com/Structure/Structure/protein-fold.html 4. Nucleic acids and proteins in one and more dimensions - second part
comparing protein structure 4. Nucleic acids and proteins in one and more dimensions - second part
comparing protein structure 4. Nucleic acids and proteins in one and more dimensions - second part
comparing protein structure 4. Nucleic acids and proteins in one and more dimensions - second part
Structural genomics NMR DNA Protein Structure Algorithm X Ray diffractometry NMR Residue THR 0.0 147.7 172.9 107.2 -125.3 187.4 CYS 123.4 63.6 103.7 PRO 60.3 83.9 -116.7 Protein Structure cryo-electron tomography DNA 0101#01001010#10111010# 01010001#10010#1001#101 10010#100100100101011#0 Algorithm 3. genome analysis
from structural knowledge to structural predictions 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction CHOU & FASMAN Chou, P.Y. & Fasman, G.D. (1974). Biochemistry, 13, 211-222. 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction # residues in window: 6 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST). 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
secondary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
Sequence Alignment “Two homologous sequences whisper ... a full multiple alignment shouts out loud.” in Hubbard TJ, Lesk AM, Tramontano A. Gathering them in to the fold. Nat Struct Biol. 1996 Apr;3(4):313.) 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
dotplot The dotplot is a simple picture that gives an overview of the similarities between two sequences. Less obvious is its close relationship to alignments. The dotplot is a table or matrix. The rows correspond to the residues of one sequence and the columns to the residues of the other sequence. In its simplest form, the positions in the dotplot are left blank if the residues are different, and filled if they match. Stretches of similar residues show up as diagonals in the upper left-lower right (Northwest-Southeast) direction. Dotplot showing identities between a repetitive sequence (ABRACADABRACADABRA) and itself. The repeats appear on several subsidiary diagonals parallel to the main diagonal. Letters corresponding to isolated matches are shown in non-bold type. The longest matching regions, shown in boldface, are the first and last names DOROTHY and HODGKIN. Shorter matching regions, such as the OTH of dorOTHy and crowfoOTHodgkin, or the RO of doROthy and cROwfoot, are noise. Dotplot showing identities between the palindromic sequence MAX I STAY AWAY AT SIX AM and itself. The palindrome reveals itself as a stretch of matches perpendicular to the main diagonal. From Introduction to Bioinformatics by Arthur M. Lesk 4. Nucleic acids and proteins in one and more dimensions - second part
http://vlab.amrita.edu/?sub=3&brch=274&sim=1434&cnt=1
4. Nucleic acids and proteins in one and more dimensions - second part
BLOSUM62 matrix does an excellent job detecting similarities in distant sequences, and this is the matrix used by default in most recent alignment applications such as BLAST 4. Nucleic acids and proteins in one and more dimensions - second part
Mutation probability matrix for the evolutionary distance of 250 PAMs 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part Amino Acid Code Meaning A Alanine B Aspartic acid or Asparagine C Cysteine D Aspartic acid E Glutamic acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine P Proline Q Glutamine R Arginine S Serine T Threonine U Selenocysteine V Valine W Tryptophan Y Tyrosine Z Glutamic acid or Glutamine X any * translation stop - gap of indeterminate length teminates with > 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
tertiary structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
ab initio calculations of protein structure Protein folding ab initio calculations of protein structure 4. Nucleic acids and proteins in one and more dimensions - second part
Metodo Assemblaggio di frammenti: Dividendo la sequenza in frammenti MSSPQAPEDGQGCGDRGDPPGDLRSVLVTTV ROSETTA Frammenti di 9 aa Sceglie le strutture delle 25 sequenze più vicine Ottimizzazione e Assemblaggio (Knowledge-based potential) 4. Nucleic acids and proteins in one and more dimensions - second part
Rosetta Fragment Libraries 25-200 fragments for each 3 and 9 residue sequence window Selected from database of known structures > 2.5Å resolution < 50% sequence identity Ranked by sequence similarity and similarity of predicted and known secondary structure 4. Nucleic acids and proteins in one and more dimensions - second part
4. Nucleic acids and proteins in one and more dimensions - second part
RNA structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part
RNA structure prediction Primary structure of RNA Secondary structure of a telomerase RNA Tertiary structure of RNA 4. Nucleic acids and proteins in one and more dimensions - second part
RNA structure prediction 4. Nucleic acids and proteins in one and more dimensions - second part