Ligands in Coot

Model-Building Proteins andLigands using X-ray DataRecent Developments in CootPaul EmsleyJune 2012

Modelling Proteins andLigands with Cootpdf available on request/from John● Overview● New algorithms and features● Tools for Ligand-handling● Putting Tools for Invention in thehands of those collecting the data● Modelling Carbohydrates

Feature IntegrationRefinementExternale.g. REFMACInternalInternalValidationExternale.g. MolProbityValidation, Model Building and Refinementshould be used together

Refinement TechniquesSingle-Atom DragOver-draggingKey-bindings:Triple RefineSingle Residue Refine with Auto-acceptRamachandran Refinement

Usage Tips: Navigation(Type) Ctrl-G : → recentres on “G”: go to blob“P”: go to nearest atom (or CA if the residue if theresidue is a standard AA)“L” (unlabel) the atom at the screen centre“O” jump to other NCS chain“V”: Undo symmetry view“Go To Ligand” (icon) → Jump to (next) ligand

Usage Tips: Use Keybindings(Noob → Pro)Built-in: “A”, “B”, “C”, “D” “F”, “Ctrl-Z”, “G”, “I”, “M”,“N”, “O”, “P”, “S”, “U”,“Ctrl-Z”, “”(My personal set): “Shift A”, “Shift B”, “E”, “Shift E”,“H”, “J”, “Shift J”, “K”, “Shift K”, “Shift M”, “Shift P”,“Q”, “Shift Q”, “R”, “Shift R”, “T”, “Shift T”, V”, “ShiftV”, “W”, “Shift W”, “X”, “Y”, “Shift 4”, “”,“(You can download these from the Coot Wiki)

Using NVIDIA CardsFor antialiasing:setenv __GL_FSAA_MODE nwhere n is 5 (or so)

Low ResolutionModel-BuildingRamachandran Optimization“Backrub” rotamers

Previous

To turn it on...(ROTAMERSEARCHLOWRES)

Networking...PDBe interface...Drag and dropAlso with drugbank19/80

PDBe Recent StructuresJSON parser, network threaded code

Using the API21/80

RCrane: Semi-AutomatedBuilding of RNA

RCrane: Semi-AutomatedBuilding of RNA

Finding HolesAn implementation ofSmart, Goodfellow & Wallace (1993)Biophysics Journal 65, 2455Atomic radii from AMBERI usedradii from CCP4 monomer librarysans simulated annealing

Ligands Tools in Coot“What should we make next?”Tools for drug discoveryParticularly fragment-based25/80

Ligands in CootImporting and building ligand from scratchPRODRG, LIBCHECK(Ligand Fitting)ValidationMogulRepresentationAnalysisBond ordersSurfacesMolprobity, LIDIA26/80

2D Ligand BuilderFree sketchSbase search

”Yesterday's” LigandCommon subgraph isomorphism, Krissinel & Henrick (2004)Atom name matchingTorsion matchingLigand overlay

Cocktail Examples

Ligand ValidationCompare the observed structure to therestraintsIn Coot: Validate → Geometry analysis

Parmatisation issues...(what if they are wrong?)Perfect refinement with incorrect parameters →distorted structureCSD's MogulKnowledge-base of geometricparameters based on the CSDCan be run as a “batch job”Mean, median, mode,quartiles, Z-scores.

Ligand ValidationMogul plugin in CootRun mogul, graphical display of resultsUpdate restraints (target and esds for bondsand angles)

Ligand RepresenationBond orders (from dictionary)

Binding mode analysisBinding site highlighting,Isolated Molprobity probe dots

Chemical Features

Ligand OverlaysIncluding maps, mean and varianceChemical Feature Clustering

Chiral Centre InversionInverted chiral centrerefinement pathologydetectionHydrogen tunnelling

Ligand Environment Layout2d Ligand pocket layout (ligplot, poseview)Can we do better? - Interactivity?

Ligand Environment LayoutBinding pocket residuesInteractionsSolvent accessibilityhalosSolvent exclusion by ligandSubstitution contour

Solvent ExposureIdentification of solvent accessible atoms

Ligand Enviroment LayoutConsiderations2D placement and distances should reflect3D metrics (as much as possible)H-bonded residues should be close theatoms to which they are bondedResidues should not overlap the ligandResidues should not overlap each otherc.f. Clark & Labute (2007)(work in progress)

Layout Energy TermsResidues match 3DDistancesResidues don'toverlay each otherResidues are closeto H-bonding ligandatomsResidues don'toverlap ligand

”Don't overlap the ligand”

Ligand Environment LayoutInitial residue placement

Optimising the minimiser

Ligand Environment LayoutResidue position minimisation

Determination of theSubstitution Contour

Substitution Contour:Extending along Hydrogens

58/80

Layout Examples

Layout Problems

Layout Examples3uic

Layout Examples3uic

Layout Examplesrosiglitazone,4a7a

Layout Problems

Protein-Protein Interface LayoutMock-up!

Modelling CarbohydratesValidation,Model-building,Refinement

Problematic GlycoproteinsCrispin, Stuart & Jones (2007)NSB Correspondence“one third of entries contain significant errors incarbohydrate stereochemistry...”“carbohydrate-specific building and validation toolscapable of guiding and construction of biologicallyrelevant stereochemically accurate models shouldbe integrated into popular crystallographicsoftware. Rigorous treatment of the structuralbiology of glycosylation can only enhance theanalysis of glycoproteins and our understanding oftheir function”PDB curators concur

Carbohydrate LinksThomas Lütteke (2007)

Validate the Links

Refinement Trials(NAG-ASN example)

Model-Building

Technical Details

Acknowldegments,CollaboratorsBernhardLohkampKevinCowtanEugeneKrissinelStuartMcNicholasMartinNobleAlexeiVagin

AcknowledgementsKeith WilsonEleanor DodsonGarib MurshudovMax CrispinAndrei LebedevLibraries, dictionariesAlexei VaginKevin CowtanEugene KrissinelJane and Dave Richardson (Duke)Greg LandrumFundingBBSRC &