navigating bioluminate for pymol users: a practical … · navigating bioluminate for pymol users:...

Navigating BioLuminate for PyMOL Users: A Practical Approach

2nd European Life Science BootcampAna Negri, PhD

Agenda•  Introduction to BioLuminate

•  PyMOL-like features in the BioLuminate interface:–  Basic rendering and visualization using BioLuminate

•  Beyond visualization: –  Antibody Modeling and Protein-Protein Docking–  Residue Mutation and Affinity Maturation

•  Hands-on tutorial: Visualization, Sequence Analysis, and Modeling with BioLuminate: A case Study with Neuraminidase

•  Questions

20’

20’

10’

Introduction to BioLuminate•  BioLuminate is the Schrödinger biologics software platform•  A suitably low learning curve for new users, non expert users•  Focused on workflows and tasks, with multiple modeling features•  GUI modeled on PyMOL

Antibody

Antigen

•  Structure prediction from sequence, humanization

Antibody design

•  Residue scanning (affinity / stability); Cysteine scanning; Protein crosslinking; In silico affinity maturation; Non-standard amino acids; Protein FEP

Protein design

•  Aggregation propensity ID; Reactive residue ID (glycosylation, proteolysis, oxidation, deamination); Peptide QSAR; Titration curve / Isoelectric point; Solubility

Protein liability ID

•  Homology modeling•  Protein-protein docking; Prime de novo loop modeling•  Protein interaction analysis; Chimeric model generation; Automated peptide docking•  Advanced sequence viewer (MSV); Automated protein quality report•  Molecular Dynamics, minimization, quantum mechanics, etc

Protein modeling

Functionality groups in BioLuminate





•  Questions

PyMOL-like features in the BioLuminate interface





•  Questions

Antibody Modeling and Protein-Protein Docking

Piper/Cluspro

FAB13B5

HIV-1 Capsid Protein (P24)

Green=xrayBlue/Maroon=predict

Orange=xray (1E6J)Blue/Green/Red=predictThird ranked complex shown

CAPRI rankings (Nir London, Rosetta Design Group, 2010)

(1A43)

(in BioLuminate)

Antibody Modeling – CDR Prediction: Input & Framework

•  Antibody-specific workflow•  Search public or in-house structures for

templates

•  Framework selection:– Separate control over L/H chain

framework templates– Control over framework used to align

chains

Antibody Modeling – CDR Prediction: Loop Grafting

Start with fast loop lookup:•  Find largest cluster with

maximum sequence similarity• Minimize grafted loop• Optionally perform

advanced loop prediction using Prime

Antibody Modeling – Database Management

• Multiple databases can be created and later selected• New structures can be added

to existing or new DB

• Licensed from Vajda group at Boston University– Kozakov et al. (2006) Proteins: Struct, Funct, Bioinf 65 392-406

• #1 server in most recent CAPRI competition– Competitive with human groups

CAPRI rankings (Nir London, Rosetta Design Group, 2010)

Piper/Cluspro: •  #1 group•  #1 server

Protein-Protein Docking

Protein-Protein Docking is Easy to Run

Antibody/Antigen Complex: Predicted Versus Experiment

Modeled FAB13B5 CDR docked with crystal structure of unbound antigen P24 (orange) versus x-ray complex 1E6J. 3rd ranked complex shown.

Residue Scanning: ID mutations for improved affinity / stability

•  Residue scanning is a technique used to determine the contribution of a specific residue to the stability, binding or function of a given protein

•  Walk mutation R→Ala along sequence

•  Tells us what mutations may be beneficial, and what may be harmful

•  Can be a very laborious and difficult task to do in the lab.

Measure

Δ AffinityΔ Stability

•  Implicit solvent (Generalized Born)

•  Rigorous all atom force field model

•  Extensively validated for protein structure prediction

•  Collaborative effort: Schrödinger, Rich Friesner (Columbia) and Matt Jacobson (UCSF)

MM-GBSA residue mutation calculations

Select residues to mutate

Calculate relevant energies

Apply equations from statistical mechanics

(Output) Free energies from mutation

Prime energy function

From Residue Scanning to Affinity Maturation

Protein 1

Protein 2

Protein 1

Protein 2

Protein 1

Protein 2

Protein 1

Protein 2

Residue Scanning (single mutations):

Affinity Maturation/Protein Design (multiple simultaneous mutations):

Affinity Maturation in BioLuminate

•  Search multiple residue positions simultaneously for changes

•  Implicit solvent MM-GBSA model•  Uses Monte Carlo sampling due to

combinatorial explosion•  Use to suggest new sequences, or to

influence random library design

Affinity Maturation in BioLuminate

Reveals positions and

types of beneficial mutations





•  Questions

Useful Video Links – Related to Today’s Webinar•  Biologics modeling tutorial series:

–  Intro to BioLuminate –  Homology Modeling (Antibody modeling)–  Residue Scanning–  Protein-Protein Docking, etc

–  http://www.schrodinger.com/videos/3

Other Useful Resources•  Schrödinger support: [email protected]

•  Knowledge Base: http://www.schrodinger.com/kb/

•  Support Center and Training Videos: http://www.schrodinger.com/supportcenter/

•  Schrödinger Seminar Series: http://www.schrodinger.com/seminarcenter/

•  Script Center: https://www.schrodinger.com/scriptcenter/

Thanks for Joining Us!

Questions?

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