X-ray structures of proteins do not in general include hydrogen atom coordinates ... its t rotamer (picture at right) distribution of. valine rotamers. in ...
Title: Gene Ontology (GO) Author: Victor A Simossis Last modified by: heringa Created Date: 2/3/2004 12:07:02 PM Document presentation format: On-screen Show (4:3)
C E N T R F O R I N T E G R A T I V E E B I O I N F O R M A T I C S V U Bioinformatics Master Course DNA/Protein Structure-function Analysis and Prediction Lecture 10 ...
remove side chains whose position may be in doubt using a number of filters, ... Modelling new IgM structure using two templates and an antigen (peptide ligand) ...
Ribose. YPVDLKLVVKQ binding protein. Modify sequence TNT. to change structure binding ... Side chain angles are defined moving outward from the backbone, starting ...
Two aligned proteins' The 8' Steps of Modelling. 1 Detect template. 2 Get alignment ... Keep only model and template. How to align: ASASASASASAS. YPYPYPYPYPYP ...
KJM5230-H04. Drug Design: Functional groups / Pharmacological Activity ... pH duodenum ca. 4. pH urine ca. 6. Identification of acidic / basic functional groups ...
Consider PSP as performing a search through the configuration space of the given ... This is needed as trying to solve PSP is too complex for real proteins ...
Protein/Nu-cleic Acid Complexes. Proteins, Peptides, Viruses. Molecular Type --Feb 5, 2002 ... Assignment 3: Construction and Analysis of the Pentapeptide Met ...
There are 20 different amino acids that can be part of the chain. ... Bond, angle, dihedral. i , j are positions in sequence. Ri is rotamer choice at position i ...
Goals for Today Introduce automated refinement and validation. Evaluate Rwork and Rfree for your ProK model. Refine ProK (automatic) Validate ProK (web server)
Title: Slide 1 Last modified by: Eugene E Kwan Created Date: 8/15/2002 9:50:45 PM Document presentation format: On-screen Show Company: McMaster University
Molecular Strain (DNA) Enthalpic-entropic compensation: DNA binding events with similar affinities ... Sequence-dependent energies of DNA deformation: ...
Title: Homology Modeling: principles, tools and techniques Author: supa Last modified by: Muhammed Sayed Created Date: 6/15/2002 7:21:30 AM Document presentation format
Homology Modeling Homology Modeling Presentation Fold recognition Model building Loop building Sidechain modeling Refinement Testing methods: the CASP experiment ...
Estereochemistry comprises empirical information about chemical interactions ... CHIRALITY of a-carbons. PLANARITY of peptide bonds and aromatic side chains ...
Sometimes a few SSEs may be missing. Fold classification: structural similarity between folds is searched using ... Domains defined with SCOP and CATH ...
Structural Bioinformatics. What is it ? What can it do for us ? Genomics ... Structural Bioinformatics. What does it do? If there is an experimental structure ...
Ab initio folding. Homology modeling. Protein threading. Stage 2: Loop Modeling ... ab. ac. clk. c. f. fgh. ij. remove dem. Side-Chain Packing Algorithm ...
Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function Ryan M Harrison, Jeffrey J Gray Baltimore Polytechnic Institute
CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS TECHNICAL UNIVERSITY ... techniques to reduce time (from months to days) and cost (from $100.000 to $20.000/structure) ...
Only few DOFs are changed at each step. Large sub-chains remain rigid between steps ... efficiency of MCS by reducing average time to accept/reject a new conformation ...
Anfinsen (1950's) showed reversibility of denaturation with urea ... hydrophobicity? presence of a clearly-defined (deep) energy minimum. ends. can't move ...
http://biochemistry.utoronto.ca/steipe/bioinformatics. Work through the Rasmol tutorial ! ... structure alignment and analysis of sequence alignments. ...
... antibody-like properties Vitamin b12-binding RNA aptamer Slide 10 Let the immune system make enzymes for you Wedemayer et al. (1997) Science 276, 1665-1669.
Bond lengths, bond angles, chirality, omega angles, side chain planarity. Overall quality: ... Distorted C -chirality. D-amino acid. Chris Spronk CMBI 2003 ...
... and include the distance, angle and dihedral values ... Stereochemical bond, angle, dihedral, improper. Homology mainchain and sidechain dihedrals ...
Automated phase improvement and model building with Parrot and Buccaneer Kevin Cowtan cowtan@ysbl.york.ac.uk X-ray structure solution pipeline... Density modification ...
Sequence alignment is the single most important step in homology modeling. ... LIG. Complete: Add ligands, substrates etc. to model. Analyse: Interpret and conclude ...
Modeling conformational changes during docking Martin Zacharias Physik-Department T38 Technische Universit t M nchen ALGORITHMS IN STRUCTURAL BIOINFORMATICS ...
The Biological Physics of Protein Folding: the Random Energy Model and ... Including hydrophobicity: -the 21th species is the water -in the 'empty' sites ...
Time scales and molecular motions. Atomic fluctuations, vibrations. ... 13C Chemical Shift Anisotropy. z. y. x. O. C. O. C. O. C. Many orientations in xy plane ...