The Curious Engineer

All blogs / Science

Oxford Protein Informatics Group

blopig.com/blog

or "OPIG" to friends

ScienceAI / MLPython

’15’20’25
Posts
983 from 11 Jan 2013 to 30 Oct 2026
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weekly (70 in the last year)
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2026 63

  1. Stop using win rate: comparing model rankings across different benchmark tasks
  2. Atom14 and Atom37: how protein design models write down atoms
  3. Lessons in Bemistry: identifying the signature of a medicinal chemist
  4. Characterising nanobody developability to improve therapeutic design using the Therapeutic Nanobody Profiler
  5. OAS-nano: New Repertoire Database Just Dropped
  6. Le Tour De Farce v13.0
  7. The First OpenBind Blind Challenge
  8. AI can remove typing. It cannot remove thinking.​
  9. Finally solving drug discovery with a Fly
  10. OPunting 2026
  11. One Year Down: Wisdom from a Former OPIG Newbie
  12. Is the race for AGI a scam? Are the tech bros con men or visionaries?
  13. Predicting ADME Properties with Machine Learning: 82% of the Performance From Two Descriptors
  14. Project Cybersyn: Bayesian Socialist Algocracy in 1970s Chile
  15. The cost of a better pose: balancing GNINA sampling and runtime
  16. Beyond the Vaccine: AI’s Expanding Role in LNP mediated Drug Delivery
  17. Claude now watermarks its text: here’s what is actually happening under the hood
  18. Oxford Agent Escapes Lab, Infiltrates EPFL, and Roams Swiss Alps
  19. Diffusion Models Can’t Give You a Likelihood… So How Do We Score Inverse-Folded Sequences?
  20. The IMGT just became a little FAIRer
  21. Work Hard, Play Hard: Balancing Sport and Studies at Oxford
  22. App-ready databases from Python with SQLModel and FastAPI
  23. Same science, different stories: writing papers vs writing grants
  24. OPIGlet’s First Conference: PEGS Boston 2026
  25. OPIG Retreat, 2026: Heatwave Edition
  26. SAbDab2: The structural antibody database in the age of machine learning
  27. Building an Agent – Practical Notes for Beginners
  28. Networks beyond proteins: a Lake Como summer school
  29. How Unusual Is Your Generated Molecule? Let The CCDC Tell You
  30. Peering Inside the Black Box: A Beginner’s Introduction to Mechanistic Interpretability
  31. A timeline of sampling methods of diffusion models
  32. Spin Lattices and Proteins – How state-based discretisations have enabled modern protein modelling
  33. Will TurboQuant save us from the RAM apocalypse?
  34. The Open Immune Window: Notes on Sweaty Workouts and Vanishing Immune Cells
  35. Revealing Nature’s Quantum Compass – Kickoff Day
  36. Three Resources I Keep Coming Back to for Learning Deep Learning
  37. What I wish I knew before applying and moving to Oxford from the US
  38. A Golden Age of Nanomedicine
  39. A first for PROTACs
  40. Curiosity might not kill the cat
  41. Speeding up python through profiling
  42. Pitfalls of AI-Generated Reviews: Case Study of a Frontiers in Microbiology Review on Anti-Influenza A bnAbs
  43. Analyzing AlphaFold 3’s Diffusion Trajectory
  44. No Pretraining, No Equivariant Architecture – Learning MLIPs without Explicit Equivariance
  45. Biologic Summit 2026
  46. Not-Proteins in Parliament: Part II
  47. SigmaDock: untwisting molecular docking with fragment-based SE(3) diffusion
  48. Fragment-to-Lead Successes in 2024 – 10th Anniversary Edition
  49. Misconduct, Bias or Benign? A Case of Missing Ångströms
  50. Why is Wikipedia so good?
  51. Potholes: an ancient problem demanding modern solutions
  52. Nice TCR processing libraries
  53. Building a “Second Brain” – A Functional Knowledge Stack with Obsidian
  54. New DPhil/PhD Programme in Pharmaceutical Science Joint with GSK!
  55. Creating scientific figures in Inkscape
  56. Advanced PyMOL Visualization for Weighted Structural Ensembles (Part 1): Ensemble Comparison
  57. Advanced PyMOL Visualization for Weighted Structural Ensembles (Part 2): Efficient Weighted SASA Surfaces
  58. Democratising the Dark Arts: Writing Triton Kernels with Claude
  59. What Molecular ML Can Learn from the Vision Community’s Representation Revolution
  60. Scientific Acceleration with Agentic Coding in 2026
  61. Can we make Boltz predict allosteric binding?
  62. Agentic AI
  63. Finding 250GB of Missing Storage On My Mac: A Warning For Large Dataset Users

2025 78

  1. The Experimentally Relevant Future of Molecular Dynamics: Lessons from the Annual Danish Workshop on Advanced Molecular Simulations
  2. Chemical Languages in Machine Learning
  3. Some thoughts on molecular similarity
  4. An Introduction to the Basics of Reinforcement Learning
  5. Dispatches from Lisbon
  6. Controlling the Diffusion Denoising Process: A Molecular Show
  7. Design your very own drug: An introduction to structure-based small molecule drug design
  8. Is the molecule in the computer?
  9. I Prompt, Therefore I Am: Is Artificial Intelligence the End of Human Thought?
  10. Nanobodies® galore in Utrecht
  11. Using Node-RED as a front-end to your software
  12. 3 Reasons Why You Should Play Chess Instead of Doing Your Work
  13. Fragment-to-Lead Successes in 2023
  14. Are you addicted to dopamine?
  15. Human Learning in the age of Machine Learning
  16. Bye Bye Lucy Vost! (Lucy Gone-st but not forgotten)
  17. Getting In the Flow – How to Flow (Match)
  18. Is attention all you need for protein folding?
  19. Extracting 3D Pharmacophore Points with RDKit
  20. Reflections on GRC CADD 2025: A Week of Insight, Innovation, and Baseball
  21. Exploring the Protein Data Bank programmatically
  22. Accelerating AlphaFold 3 for high-throughput structure prediction
  23. Handling OAS Scale Datasets Without The Drama
  24. Exploding Barbers (Paradoxes — Part I)
  25. A guide to fixing broken AMBER MD trajectory files and visualisations.
  26. Understand Large Codebases Faster Using GitIngest
  27. ISMB/ECCB conference feedback
  28. How reliable are affinity datasets in practice?
  29. Conference feedback: Protein Society Annual Symposium
  30. GPT-5 achieves state-of-the-art chemical intelligence
  31. Installing open source PyMOL with pip
  32. Taming the Trajectory Beast: A Simpler Way to Sample Your MD Simulations
  33. OPIG website and services will undergo routine maintenance on Monday 11 August 2025 at 10:00 UTC
  34. Antibody developability datasets
  35. Publishing 101
  36. A more robust way to split data for protein-ligand tasks?
  37. GUI Slop
  38. Can AI help us design better viruses?
  39. Le Tour de Farce v12.0
  40. PEGS Boston 2025
  41. Pose Prediction: Does Your Model Generalize? The Role of Data Similarity
  42. On the Joys of vim-like Browsing
  43. Attention Is All You Need – A Moral Case
  44. Eye of the World by Robert Jordan: A Concise Review
  45. ChatGPT can now use RDKit!
  46. Estimating uncertainty in MD observables using block averaging
  47. Memory Efficient Clustering of Large Protein Trajectory Ensembles
  48. Open Source Pharma: From Idealism to Pragmatic Solutions
  49. An insight into mega-conferences – attending ESCMID Global 2025
  50. Attending LMRL @ ICLR 2025
  51. Interested in Research Software Engineering? We’re hiring!
  52. Demystifying Git and Merge Conflicts
  53. Cheating at Spelling Bee using the command line
  54. Featurisation is Key: One Version Change that Halved DiffDock’s Performance
  55. Slurm and Snakemake: a match made in HPC heaven
  56. A Masterclass in Basic & Translational Immunology with Prof. Abul Abbas
  57. AI generated linkers™: a tutorial
  58. NVIDIA Reimagines CUDA for Python Developers
  59. Debugging code for science: Fantastic Bugs and Where to Find Them.
  60. GUI Science
  61. LOADING: an art and science collaborative project
  62. Holding out for a GPU
  63. The business of health: research and funding from academia to big pharma
  64. Therapeutic antibodies and their function
  65. AI in Academic Writing: Ethical Considerations and Best Practices
  66. Confidence in ML models
  67. The Sprawl: Slogs in Scribing and Software
  68. Combining Multiple Comparisons Similarity plots for statistical tests
  69. Geometric Deep Learning meets Forces & Equilibrium
  70. The Good (and limitations) of using a Local CoPilot with Ollama
  71. Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data
  72. Estimating the Generalisability of Machine Learning Models in Drug Discovery
  73. LLM Coding Tools – An Overview
  74. De novo protein padlocks
  75. Molecule Networks: data visualization using PyVis
  76. Baby’s First NeurIPS: A Survival Guide for Conference Newbies
  77. Diagnostics on the Cutting Edge, Software in the Stone Age: A Microbiology Story
  78. Making pretty, interactive graphs the simple way – Use Plotly.

2024 99

  1. A tougher molecular data split – spectral split
  2. Generating Haikus with Llama 3.2
  3. Visualising and validating differences between machine learning models on small benchmark datasets
  4. Making Pretty Pictures in PyMOL v2
  5. Controlling PyMol from afar
  6. Building CLI Applications with Typer
  7. Cross referencing across LaTeX documents in one project
  8. Using Jupyter on a remote slurm cluster
  9. Big Compute doesnt want you to know this! Maximising GPU Usage with CUDA MPS
  10. Cream, Compression, and Complexity: Notes from a Coffee-Induced Rabbit Hole
  11. Op uns
  12. Maybe we should train on our test set?
  13. The “AI-ntibody” Competition: benchmarking in silico antibody screening/design
  14. Making Peace with Molecular Entropy
  15. Navigating Hallucinations in Large Language Models: A Simple Guide
  16. Protein Property Prediction Using Graph Neural Networks
  17. Testing python (or any!) command line applications
  18. The XChem trove of protein–small-molecules structures not in the PDB
  19. Why the vegans will say “I told you so…”
  20. Aider and Cheap, Free, and Local LLMs
  21. MDAnalysis: Work with dynamics trajectories of proteins
  22. Our future health: A new UK health research programme
  23. Walk through a cell
  24. Out of the box RDKit-valid is an imperfect metric: a review of the KekulizeException and nitrogen protonation to correct this
  25. The Patterns that Escape Us
  26. Drug Discovery Tools, but they’re olympic sports…
  27. Do not forget to add your data folder to .gitignore
  28. Tanimoto similarity of ECFPs with RDKit: Common pitfalls
  29. I really hope my compounds get the green light
  30. Roche Continents 2024
  31. The wider applications of nanobodies
  32. Making your code pip installable
  33. Five-word stories about a world where AI dominates the world
  34. My CCDC Science Day Experience
  35. Happily hallucinating (for humans)
  36. Memory-mapped files for efficient data processing
  37. OPunting 2024
  38. Converting or renaming files, whilst still maintaining the directory structure
  39. Experience at the Computational Chemistry Gordon Research Conference
  40. Sort and Slice Tutorial – An alternative to extended connectivity fingerprints
  41. ggPlotting tips with OPIG data
  42. Conference Summary: AIRR Community Meeting VII – Learnings and Perspectives
  43. Incorporating conformer ensembles for better molecular representation learning
  44. Reproducible publishing
  45. Architectural highlights of AlphaFold3
  46. Le Tour de Farce v11.0
  47. The Tale of the Undead Logger
  48. Deliberately misfolding prions to find the golden thread.
  49. Easy Python job queues with RQ
  50. Conformational Diversity in Proteins, Revisited
  51. Conference summary: Generative AI in Life Science
  52. My take on the Collaborations Workshop (CW) 2024
  53. Interactive visualization of protein–ligand complexes with Py3Dmol
  54. Comparing pose and affinity prediction methods for follow-up designs from fragments
  55. Fine-tune generated molecular poses with a force field
  56. Organise Your ML Projects With Hydra
  57. Environmentally sustainable computing
  58. The War of the Roses: Tea Edition
  59. Paths that you need to know for compiling
  60. Pyrosetta for RFdiffusion
  61. Exploring multilingual programming
  62. Mounting a remote file system with SSHFS
  63. Quickly (and lazily) scale your data processing in Python
  64. Mapping derivative compounds to parent hits
  65. Conference Summary: MGMS Adaptive Immune Receptors Meeting 2024
  66. How to write a review paper as a first year PhD student
  67. How can FemTech help close the gender health gap?
  68. Inverse Vaccines
  69. Using JAX and Haiku to build a Graph Neural Network
  70. Useful metrics and their meanings
  71. Dockerized Colabfold for large-scale batch predictions
  72. Tracking the change in ML performance for popular small molecule benchmarks
  73. RSC Fragments 2024
  74. Under-rated or overlooked, these libraries might be helpful.
  75. Pitfalls of using Pearson’s correlation for comparing model performance
  76. Open Source PyMOL installation on Windows
  77. An Open-Source CUDA for AMD GPUs – ZLUDA
  78. Optimising for PR AUC vs ROC AUC – an intuitive understanding
  79. 3 approaches to linear-memory Transformers
  80. Fail fast
  81. Making your figures more accessible
  82. Plotext: The Matplotlib Lookalike That Breaks Free from X Servers
  83. In defence of chaos
  84. Working with PDB Structures in Pandas
  85. Navigating the world of GNN layers with PyTorch Geometric
  86. 250 Trips on the Oxford Tube: what I’ve learnt
  87. Optimising Transformer Training
  88. How to make ML your entire personality
  89. A Seq2Seq model for ETF forecasting
  90. Tip and Tricks to correct a Cuda Toolkit installation in Conda
  91. AlphaGeometry: are computers taking over math?
  92. The stuff MDAnalysis didn’t implement: CPU Parallel HOLE conductance analysis
  93. Taking Equivariance in deep learning for a spin?
  94. PhD as a mother
  95. OPIGmas, 2023
  96. On National AI strategies
  97. Antibody Engineering & Therapeutics 2023
  98. How to get more information from slurm?
  99. Finding and testing a reaction SMARTS pattern for any reaction

2023 87

  1. Online tools for drawing and visualizing molecules
  2. Handy LaTeX syntax I Googled over the years
  3. Some useful pandas functions
  4. The Antibody Dictionary
  5. Let your library design blosum
  6. How to replace bike ball bearings when your steering sounds crunchy
  7. VHH -vs- VNAR
  8. Where do we go from here?
  9. The workings of Fragmenstein’s RDKit neighbour-aware minimisation
  10. Converting pandas DataFrames into Publication-Ready Tables
  11. Demystifying the thermodynamics of ligand binding
  12. What the heck are TPUs?
  13. OPIG: A decade of Scientific Shenanigans. What’s changed?
  14. Deploying a Flask app part II: using an Apache reverse proxy
  15. Understanding GPU parallelization in deep learning
  16. Understanding positional encoding in Transformers
  17. Conference feedback: AI in Chemistry 2023
  18. Antibody Engineering & Therapeutics Europe 2024
  19. SSH, the boss-fight level: Jupyter notebooks from compute nodes
  20. Conference feedback — with a difference
  21. Deploying a Flask app part I: the gunicorn WSGI server
  22. Thera-SAbDab Updates (2023)
  23. Tips & tricks with PyMOL
  24. GitHub.dev: Just press “.”
  25. Out of Band Management
  26. The Surprising Shape of Normal Distributions in High Dimensions
  27. Current strategies to predict structures of multiple protein conformational states
  28. OPIG Retreat 2023
  29. LightningCLI, my new best friend
  30. A Simple Way to Quantify the Similarity Between Two Sets of Molecules
  31. AI Can’t Believe It’s Not Butter
  32. A simple criterion can conceal a multitude of chemical and structural sins
  33. The Notorious O.P.I.G go punting
  34. Placeholder compounds: distraction vs. accuracy
  35. ggPlotting tips with OPIG data
  36. The dangers of Conda-Pack and OpenMM
  37. Lucubration or Gaslighting?​
  38. Cosmology via Structural Biology and Half-Lives of Teaspoons: Bizarre Papers from Around the Internet
  39. What can you do with the OPIG Immunoinformatics Suite? v3.0
  40. A match made in heaven: academic writing with latex and git
  41. “The Rise of ChatGPT 4.0: Is the Future of Work in Jeopardy?”
  42. PHinally PHunctionalising my PHigures with PHATE feat. Plotly Express.
  43. Le Tour de Farce 2023
  44. KAUST Computational Advances in Structural Biology
  45. 9th Joint Sheffield Conference on Cheminformatics
  46. Customising MCS mapping in RDKit
  47. Machine learning strategies to overcome limited data availability
  48. Exploring the Observed Antibody Space (OAS)
  49. Academic Reading? There’s an AI for that.
  50. Pairwise sequence identity and Tanimoto similarity in PDBbind
  51. Checking your PDB file for clashing atoms
  52. Streamlining Your Terminal Commands With Custom Bash Functions and Aliases
  53. Unclear documentation? ChatGPT can help!
  54. Cross-linking mass-spectrometry: a guide to conformational confusions.
  55. Coding a Progress Bar for your Google Slides Presentation
  56. Writing a BLOPIG Post With ChatGPT: A Personal Take on Using AI for Assisted Writing
  57. Train Your Own Protein Language Model In Just a Few Lines of Code
  58. The State of Computational Protein Design
  59. How ChatGPT changed my writing as an ESL speaker
  60. Useful small molecules blogs
  61. Be a computational chemist and you must be a jack of all trades
  62. Better histograms with Python
  63. BRICS Decomposition in 3D
  64. AI-pril Fools
  65. An Overview of Clustering Algorithms
  66. PLIP on PDBbind with Python
  67. Molecular conformation generation with a DL-based force field
  68. The ultimate modulefile for conda
  69. BRICS Decomposition and Synthetic Accessibility
  70. Experience at a Keystone Symposium
  71. Ligands of CASF-2016
  72. Can AlphaFold predict protein-protein interfaces?
  73. LaTeX Beamer Template with Logos
  74. Atom mapping with RXNMapper
  75. How to easily use pharmacophoric atom features to turn ECFPs into FCFPs
  76. Writing “vector trajectories” with cpptraj
  77. The Most ReLU-iable Activation Function?
  78. SnackGPT
  79. SUMO wrestling with developability
  80. Datamining Wikipedia and writing JS with ChatGTP just to swap the colours on university logos…
  81. Creating a Personal Website
  82. Some ponderings on generalisability
  83. Happy 10th Birthday, Blopig!
  84. Can ChatGPT write my abstract for me?
  85. SAbBox in 2023: ImmuneBuilder and more!
  86. The Boltzmann Distribution and Gender Stereotypes
  87. Three months in industry and returning to my PhD

2022 99

  1. Quality Stats
  2. The exotic zoo of antibodies
  3. Does ChatGPT know how to translate images?
  4. Two useful modules to help you find the best ML model for your task
  5. Festival of Biologics 2022 – November 2-4 Basel, Switzerland
  6. Bad chemistry in old protein-ligand binding complex data set?
  7. histo.fyi: A Useful New Database of Peptide:Major Histocompatibility Complex (pMHC) Structures
  8. Some Musings on AI in Art, Music and Protein Design
  9. Cleaning outliers in conductance timeseries from molecular dynamics
  10. A ChatGPT rap battle
  11. Modeling as a way of trying to be less surprised
  12. CodeQL analyses your code to find common errors
  13. How to turn a SMILES string into an extended-connectivity fingerprint using RDKit
  14. Unreasonably faster notes, with command-line fuzzy search
  15. Naga101: A Guide to Getting Started with (OPIG) Slurm Servers
  16. Coarse-grained models of antibody solutions
  17. Supercharge Your Literature Review With These Tools
  18. Thinking of going to a conference
  19. Am I better? Performance metrics unravelled
  20. Code your own molecule sketcher in 4 easy steps!
  21. How to build a Python dictionary of residues for each molecule in PyMOL
  22. Tales of an OPIG Jamboree
  23. Llamas and nanobodies
  24. Graphormer: Merging GNNs and Transformers for Cheminformatics
  25. Using Conda environments with Flask and Apache
  26. Running code that fails with style
  27. Universal graph pooling for GNNs
  28. Musings on Digital Nomaddery from Seoul
  29. 5th AI in Chemistry meeting
  30. Vaccines and vino
  31. An evolutionary lens for understanding cancer and its treatment
  32. How to make your own singularity container zero fuss!
  33. Identify Silly Molecules
  34. Automatic argument parsers for python
  35. Do you have cis peptide bonds in your simulation inputs?
  36. Words of Wisdom from final year PhD students
  37. Tidbits from YouGov Polls
  38. OPIG swag poll results
  39. Retrieving AlphaFold models from AlphaFoldDB
  40. Ten quick tips for proofreading your work
  41. Filtering molecules with long linkers
  42. Meeko: Docking straight from SMILES string
  43. ISMB 2022 – July 10-14 Madison, Wisconsin
  44. 5th Artificial Intelligence in Chemistry Symposium
  45. The evolution, evolvability and engineering of gene regulatory DNA
  46. The SARS-CoV-2 protein spike glycosylation not only shields but primes binding by providing structural stability too
  47. Cool ideas in Deep Learning and where to find more about them
  48. Monoclonal antibody PRNP100 therapy for Creutzfeldt–Jakob disease
  49. Le Tour de Farce v9.0
  50. Exploring topological fingerprints in RDKit
  51. Tackling horizontal and vertical limitations
  52. Oxford MRC DTP Symposium 2022
  53. Entering a Stable Relationship with your Neural Network
  54. AIRR Community Meeting VI May 17-19
  55. Visualise with Weight and Biases
  56. Sharing Data Responsibly: The FAIR Principles
  57. Viewing fragment elaborations in RDKit
  58. Antibodies as Drugs: Keystone Symposia
  59. Making better plots with matplotlib.pyplot in Python3
  60. Dealing with multiple compilers
  61. Benford’s law and OAS
  62. Congratulations to Prof. Charlotte Deane, MBE
  63. How to turn a SMILES string into a vector of molecular descriptors using RDKit
  64. GitHub actions can be useful
  65. CryoEM is now the dominant technique for solving antibody structures
  66. Why can a man not lift himself by pulling up on his bootstrap hypothesis test?
  67. Linux Horror stories vol II: Automatic drivers update
  68. Make your code do more, with less
  69. From code to molecules: The future of chemical synthesis
  70. Paper review: “EquiBind”
  71. Better Models Through Molecular Standardization
  72. Feeding a drove of hungry OPIGlets
  73. MM(PB/GB)SA – a quick start guide
  74. Einops: Powerful library for tensor operations in deep learning
  75. OPIG Retreat 2022
  76. Women in Computing: past, present and what we can do to improve the future.
  77. OpenMM Setup: Start Simulating Proteins in 5 Minutes
  78. How to prepare a molecule for RDKit
  79. How to Install Open Source PyMOL on Windows 10
  80. Making pwd redundant
  81. 3 Key Questions to Think About When Designing Proteins Computationally
  82. How to estimate the inestimable
  83. Post-processing for molecular docking: Assigning the correct bond order using RDKit.
  84. Non-linear Dependence? Mutual Information to the Rescue!
  85. Fragment Based Drug Discovery with Crystallographic Fragment Screening at XChem and Beyond
  86. Goatcrashing OPIG
  87. How to Blopig
  88. How to turn a SMILES string into a molecular graph for Pytorch Geometric
  89. NeurIPS 2021 Conference Feedback
  90. Python’s Data Classes
  91. A quantitative way to measure targeted protein degradation
  92. Tracking Changes in LaTeX
  93. What is a plantibody?
  94. Solving WORDLE with grep
  95. Simplify your life with SLURM and sync
  96. New Antibody Therapeutic INNs will no longer end in “-mab”!
  97. Stochastic chemical kinetics – things randomly bumping into each other
  98. OPIGmas 2021: Omicron Variant
  99. Antibody Engineering and Therapeutics Conference

2021 80

  1. Model validation in Crystallographic Fragment Screening
  2. snakeMAKE better workflows with your code
  3. Highlights from the European Antibody Congress 2021
  4. Targeted protein degradation phenotypic studies using HaloTag CRISPR/Cas9 endogenous target tagging and HaloPROTAC
  5. Packaging with Conda
  6. Five Nuggets of Wisdom for Chairing at a Conference
  7. New review on BCR/antibody repertoire analysis out in MAbs!
  8. A logical brain teaser to derail your afternoon
  9. Benchmarks in De Novo Drug Design
  10. An A-Z of Oxford
  11. Using normalized SuCOS scores.
  12. An idea by any other name would smell as sweet.
  13. Monty Python
  14. Getting the PDB structures of compounds in ChEMBL
  15. Issues with graph neural networks: the cracks are where the light shines through
  16. Command-Line Interfaces (CLIs), argparse.ArgumentParser and some of my tricks.
  17. Multiple Testing: What is it, why is it bad and how can we avoid it?
  18. Unraveling the role of entanglement in protein misfolding
  19. How to interact with small molecules in Jupyter Notebooks
  20. List comprehension: an elegant Python feature inspired by mathematical set theory
  21. Watch out when using PDBbind!
  22. Chained or Unchained: Markov, Nekrasov and Free Will
  23. Why all academics should be on TikTok
  24. Being Brief.
  25. Using Singularity on Windows with WSL2
  26. Lessons in Scientific Code Deployment
  27. New search features for the Structural Antibody Database (SAbDab)
  28. Antibodies for gut or bad
  29. Former OPIGlets – where are they now?
  30. 2021 likely to be a bumper year for therapeutic antibodies entering clinical trials; massive increase in new targets
  31. A Smattering of Olympic Trivia!
  32. A handful of lesser known python libraries
  33. Writing Papers in OPIG
  34. OPIGlets go flying
  35. ISMB 2021: epitope prediction tools
  36. Uniformly sampled 3D rotation matrices
  37. Making your python tool as easy to install as possible
  38. Linux Horror Stories and Protection Spells (Volume I)
  39. AlphaFold 2 is here: what’s behind the structure prediction miracle
  40. OPIGlets go Kayaking
  41. A to Z of Alternative Antibody Formats: Next-Generation Therapeutics
  42. One of my other hats – Covid-19 Response Director for UK research and innovation
  43. How fast can a protein fold?
  44. Out-of-distribution generalisation and scaffold splitting in molecular property prediction
  45. Automated intermolecular interaction detection using the ODDT Python Module
  46. The Smallest Allosteric System
  47. How do I do regression when my predictors have multicollinearity?
  48. Safety and sexism: the heroic stubbornness of Frances Oldham Kelsey
  49. Hosting multiple Flask apps using Apache/mod_wsgi
  50. Hidden Markov Models in Python: A simple Hidden Markov Model with Known Emission Matrix fitted with hmmlearn
  51. CAML: Courses in Applied Machine Learning
  52. Can few-shot language models perform bioinformatics tasks?
  53. Code that I am grateful for
  54. Do antibodies care about sex?
  55. Bioinformatics Hackathon Reflection
  56. 6 things I’ve learnt in my first year as a PhD student
  57. Singularity: a guide for the bewildered bioinformatician
  58. RNA-Seq for dummies
  59. Antibody Binding is Mediated by a Compact Vocabulary of Paratope-Epitope Interactions
  60. Is bigger better?
  61. C++ python bindings in 5 minutes
  62. Slippery slopes and slippery flats
  63. IWD 2021 and the Gender Pay Gap
  64. Better understanding of correlation
  65. ORDER!: Returning bond order information to your docked poses
  66. Commercialising your research: Where to start?
  67. Peer Review: reviewing as an early career researcher
  68. The Coronavirus Antibody Database: 10 months on, 10x the data!
  69. To Pickle, Or Not To Pickle? — Quickle!
  70. On The Logic of GOing with Weisfeiler-Lehman
  71. Ten Simple Rules For Solving Any Problem
  72. Plotly for interactive 3D plotting
  73. Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains
  74. Seaborn 101
  75. Calculating symmeterised small molecule RMSDs using graph automorphisms in python with GEMMI and NetworkX
  76. Tracking machine learning projects with Weights & Biases
  77. Miniproteins – small but mighty!
  78. Making Pretty Pictures with PyMOL
  79. Fragment-to-Lead Successes in 2019
  80. AIRR Community Meeting V – December 2020

2020 96

  1. OPIGmas 2020, Pandemic Edition
  2. An in vivo force sensor reveals varied mechanisms of co-translational force generation
  3. Prediction of Parkinson subtypes at COXIC 2020
  4. Curious About the Origins of Computerized Molecules? Free Webinar Dec 22…
  5. UMAP Visualization of SARS-CoV-2 Data in ChEMBL
  6. CASP14: what Google DeepMind’s AlphaFold 2 really achieved, and what it means for protein folding, biology and bioinformatics
  7. Drawing Wavy Lines That Match Your Data, or, An Introduction to Kernel Density Estimation
  8. BioDataScience101: a fantastic initiative to learn bioinformatics and data science
  9. Doing rigid receptor docking? Consider using multiple structures!
  10. PyMOL: colour by residue
  11. Enhance your presentation by using virtual webcams and scene transitions
  12. Graphical abstracts that spark joy on a gloomy day
  13. Using Python in PyMOL
  14. Building More Useful Bash Scripts
  15. Cryo-EM reaches atomic resolution in protein structure determination
  16. A new Graduate students (unexperienced) guide to academic literature.
  17. 3 Useful UNIX commands you might not know
  18. NeurIPS 2020: Chemistry / Biology papers
  19. Speaking about Sequence and Structure at a Summit
  20. Improving your Python code quality using git pre-commit hooks
  21. The 10 Commandments of OPIG (Lockdown edition)
  22. From Jupyter to Slides using RISE
  23. Smaller and Smaller Fragments
  24. The right tool for the job – The Joy of Excel
  25. Constrained docking for bump and hole methodology
  26. It’s been here all along: Analysis of the antibody DE loop
  27. Epitope mapping with structural data for SARS-CoV-2 RBD and 10 known binders
  28. What can you do with the OPIG Antibody Suite? v2.0
  29. Adding paired BCR data to OAS
  30. Antibody-protein binding and conformational changes
  31. PyMOL: colouring proteins by property
  32. Robust gene coexpression networks using signed distance correlation
  33. How to SCP files from a gated server to your personal computer
  34. Curing Dogs With Cancer: The Power of the Antibody
  35. Re-educating myself about the light chain
  36. C is for Cysteines (plus a fun quiz)
  37. Le Tour de Farce v8.0
  38. Understanding Conformational Entropy in Small Molecules
  39. Learning from Biased Datasets
  40. Prerecording Conference Talks and Posters using OBS Studio
  41. Pigs in the Parks: OPIG Social 28JUL2020
  42. Climate Change @ ISMB
  43. Citizen Science in Video Games
  44. Drug Promiscuity vs Selectivity
  45. Observed Antibody Space + miAIRR
  46. No labels, no problem! A quick introduction to Gaussian Mixture Models
  47. K-Means clustering made simple
  48. Real Space Correlation Coefficient
  49. ICML 2020: Chemistry / Biology papers
  50. Uploading/downloading small files across systems
  51. ProCare: cavity similarity searching and its applications to fragment-based drug design
  52. Journal Club: the Dynamics of Affinity Maturation
  53. Where do OPIGlets come from?
  54. EEGor on Proteins: A Brain-based Perspective on Crowd-sourced Protein Structure Prediction
  55. How COVID-19 affected my (undergrad) masters
  56. 10 reasons why LGBT Pride is still necessary
  57. Visualising macromolecules and grids in Jupyter Notebooks with nglview
  58. Storing variables in Jupyter Notebooks using %store magic
  59. Editors for remote development
  60. Pets can catch coronavirus too
  61. Electrostatic interactions govern extreme nascent protein ejection times from ribosomes and can delay ribosome recycling
  62. When antibodies go wrong: how antibodies can help viruses infect cells
  63. The Coronavirus Antibody Database (CoV-AbDab)
  64. More tales of 3D printing
  65. Science in the Time of COVID-19
  66. HERO proteins are here to save you (assuming you’re another protein or a fruit fly)
  67. Don’t drink bleach, don’t share canards!
  68. Non-specialist intro: Convalescent sera and some thoughts on its relevance to structural biology
  69. Understanding the synthesizability of molecules proposed by generative models
  70. DeLinker – Deep Generative Models for 3D Linker Design
  71. GEMMI: A Python Cookbook
  72. Identifying shared antibodies using deep learning
  73. Streamlining SSH for remote work
  74. TCRBuilder: Multi-state T-cell receptor structure prediction
  75. CCK-18 is Going Virtual
  76. Converting Miles to Kilometres – An inefficient but neat method
  77. Visualisation of very large high-dimensional data sets as minimum spanning trees
  78. Bayesian Optimization and Correlated Torsion Angles—in Small Molecules
  79. Lightning-fast Python code
  80. Coronavirus
  81. Considering Containers? – Go for Singularity
  82. Molecular dynamics analysis in MDAnalysis
  83. State of the art in AI for drug discovery: more wet-lab please
  84. Using SLURM a little bit more efficiently
  85. Conference feedback – MABRA workshop “Adaptive immune repertoires and beyond”
  86. Robust networks to study omics data
  87. Cooking Up a (Deep)STORM with a Little Cup of Super Resolution Microscopy
  88. Finding The Gene Responsible for Huntington’s Disease – The Story of Nancy Wexler.
  89. Effect of Debiasing Protein-Ligand binding data on Generalization
  90. The address of a gene
  91. Functional Programming in Python
  92. AutoDock 4 and AutoDock Vina
  93. Green politics, the left, and Brexit
  94. Parallelising antigen-specific B-cell isolation with LIBRA-seq
  95. B-Cell Bispecificity?!
  96. The evolution of contact prediction – a new paper

2019 75

  1. Xmas proteins
  2. Transforming Parliament – Training and deploying speech generation transformers for parliamentary speakers
  3. This Group is Tired of Comic Book Movies : An OPIGlet’s appeal to the DC and Marvel Corporations.
  4. Journal Club: Is our data biased, and should it be?
  5. IEEEGor Knows What You’re Thinking…
  6. Consistent plotting with ggplot
  7. How to be a Bayesian – ft. a completely ridiculous example
  8. de novo Small Molecule Design using Deep Learning
  9. COSTNET19 Conference
  10. You’re getting on my biscuits
  11. Common denominators between a PhD and an Oxford ball
  12. What are Hotspots in Structural Biology?
  13. Invisible Women – Exposing Data Bias in a World Designed by Men
  14. GitHub Link to Text Mining Tool
  15. SAbBox – the easy way to obtain our antibody tools
  16. Things I’ve Learned from Hosting Speaker Events
  17. Tsar Nicolas II and the curious case of the mismatched bases in his maternal mitochondrial DNA – was Tsar Nicolas II really killed in a cellar in 1917?
  18. A Gentle Introduction to the GPyOpt Module
  19. A few more reasons why UNIX is awesome
  20. Comparative analysis of the CDR loops of antigen receptors
  21. NeurIPS 2019: Chemistry/Biology papers
  22. OPIG Retreat, 2019
  23. A collection of prion factoids
  24. Le Tour de Farce v7.0 (or: How I learned to Stop Worrying and Love the Wheels)
  25. Prof. Charlotte Deane on the World Service
  26. Handling electron density in python for fun and profit
  27. Why you should care about startups as a researcher
  28. Chat bots and the Turing test
  29. Some more Python tips and tricks
  30. A new way of eating too much
  31. A Month in Basel – Summer 2019
  32. Bringing practical bioinformatics to high school classrooms
  33. When OPIGlets leave the office
  34. Three things to help you get started on Bayesian Optimisation
  35. OpenMM – easy to learn, highly flexible molecular dynamics in Python
  36. Learning dynamical information from static protein and sequencing data
  37. Combining Inset Plots with Facets using ggplot2
  38. Custom coffee mugs for OPIG
  39. Oh lord, they comin’ – a diversity of units
  40. Gene-Edited Crops
  41. Python Handout
  42. Two Tools for Systematically Compiling Ensembles of Protein Structures
  43. BOKEI: Bayesian Optimization Using Knowledge of Correlated Torsions and Expected Improvement for Conformer Generation
  44. How to Iterate in PyMOL
  45. Getting home: An ordeal of flight cancellations (& what they actually cost)
  46. Trying out some code from the Eighth Joint Sheffield Conference on Chemoinformatics: finding the most common functional groups present in the DSPL library
  47. Searching through large databases with bloom filter
  48. Which fragment first?
  49. On the Virtues of the Command Line
  50. Film review: Back to the lab
  51. Just Call Me EEGor
  52. Why you should care about type hints in Python
  53. Constrained Embedding with RDKit
  54. Modelling Conformational Flexibility of Kinases in Inactive States
  55. A Brief Introduction to ggpairs
  56. AIRR community meeting
  57. Oxford Maths Festival ‘19
  58. What is the hydrophobic-polar (HP) model?
  59. Alchemistry Free Energy Workshop 2019, Göttingen
  60. Dimensions: The Mathematics of Symmetry and Space
  61. Should scientists learn C++?
  62. Spring 2019 ACS National Meeting (Orlando)
  63. Quick Python tricks
  64. More Fun With 3D Printing
  65. Property based testing in Python with Hypothesis : how to break your own code before someone else does
  66. A gentle primer on quantum annealing
  67. A blog post about a blog
  68. Not-Proteins in Parliament
  69. Journal Club: Investigating Allostery with a lot of Crystals
  70. Some useful tools
  71. Kernel Methods are a Hot Topic in Network Feature Analysis
  72. Magnetotaxis: A Bacterial Superpower
  73. Making the most of your CPUs when using python
  74. Non-alcoholic fatty liver disease
  75. Graph-based Methods for Cheminformatics

2018 50

  1. Automated testing with doctest
  2. Because not all interesting biology is health-related!
  3. Turning MD Trajectories into Movies using PyMOL
  4. Vim and I
  5. Exciting new studies in OAS
  6. Finding the lowest energy conformation of given molecule!
  7. Check My Blob
  8. OPIG Putts Up
  9. What can you do with the OPIG Antibody Suite?
  10. docopt for dummies
  11. How to get seasick without leaving your desk
  12. Preparing a five minute conference talk: an honest account
  13. So, you are interested in compound selectivity and machine learning papers?
  14. OPunting 2018
  15. Mol2vec: Finding Chemical Meaning in 300 Dimensions
  16. Cinder: Crystallographic Tinder
  17. Rasmus Fonseca and GetContacts
  18. ISMB 2018: Collaborative Structural Biology using Machine Learning and Jupyter Notebook
  19. ISMB 2018 (Chicago): Summary of Interesting Talks/Posters
  20. Seeing the Mesoscale
  21. Covariate Shift in Virtual Screening
  22. Protein Engineering and Structure Determination
  23. Introduction to R Markdown
  24. Maps are useful. But first, you need to build, store and read a map.
  25. Le Tour de Farce v6.0
  26. Storing your stuff with clever filesystems: ZFS and tmpfs
  27. OPIG at the Oxford Maths Festival
  28. How to parse OAS data
  29. Prague Protein Spring 2018
  30. Neuronal Complexity: A Little Goes a Long Way…To Clean My Apartment
  31. The Ten Commandments of OPIG
  32. My experience with (semi-)automating organic synthesis in the lab
  33. The Curious Case Of A Human Chimera
  34. Measuring correlation
  35. OPIGTREAT
  36. New avenues in antibody engineering
  37. Helpful resources for people studying therapeutic antibodies
  38. I just wanted TensorFlow
  39. Biophysical Society 62nd Annual Meeting
  40. Working with Jupyter notebook on a remote server
  41. Dealing with indexes when processing co-evolution signals (or how to navigate through “sequence hell”)
  42. Interactive Illustration of Collaboration Networks with D3
  43. Fun with Proteins and 3D Printing!
  44. Teaching Network Science to High School Students
  45. Young Entrepreneurs Scheme (YES) Competition
  46. A short intro to machine precision and how to beat it
  47. The Seven Summits
  48. TCR Database
  49. ABodyBuilder and model quality
  50. Crystallographic programming: Super short tour of the cctbx

2017 47

  1. Paper review: “Inside the black box”
  2. Journal Club: Large-scale structure prediction by improved contact predictions and model quality assessment.
  3. Latexing with gvim
  4. Journal Club post: Interface between Ig-seq and antibody modelling
  5. Journal club: Human enterovirus 71 protein interaction network prompts antiviral drug repositioning
  6. Drawing Networks in LaTeX with tikz-network
  7. Comparing naive and immunised antibody repertoire
  8. Proteins evolve on the edge of supramolecular self-assembly
  9. Slowing the progress of prion diseases
  10. Journal Club: Statistical database analysis of the role of loop dynamics for protein-protein complex formation and allostery
  11. Typography in graphs.
  12. Using Random Forests in Python with Scikit-Learn
  13. Biological Space – a starting point in in-silico drug design and in experimentally exploring biological systems
  14. In MATLAB, it’s colormaps all the way down
  15. A Day in the Life of a DPhil Student… that also rows for Oxford.
  16. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?
  17. Antibody Developability: Experimental Screening Assays
  18. Le Tour de Farce v5.0
  19. Computational immunogenicity reduction
  20. Computationally designing antibodies using a known binding motif
  21. Using bare git repos
  22. Experimental Binding Modes of Small Molecules in Protein-Ligand Docking
  23. A brief history of usage of the word “decoy” in protein structure prediction
  24. Conformational diversity analysis reveals three functional mechanisms in proteins
  25. Interesting Antibody Papers
  26. Protein structure determination using metagenome sequence data
  27. Bitbucket and PyCharm – Tools to make a DPhil less problematic
  28. Colour page counter
  29. Faster FREAD with Pandas
  30. A very basic introduction to Random Forests using R
  31. Interesting Antibody Papers
  32. Biophysical Society 61st Annual Meeting – New Orleans, February 2017
  33. Using Antibody Next Generation Sequencing data to aid antibody engineering
  34. Multiomics data analysis
  35. Protein Structure Classification: Order in the Chaos
  36. Prions
  37. Parallel Computing: GNU Parallel
  38. Interesting Jupyter and IPython Notebooks
  39. Interesting Antibody Papers
  40. Using RDKit to load ligand SDFs into Pandas DataFrames
  41. R or Python for data vis?
  42. Confidence (scores) in STRING
  43. Interesting Antibody Papers
  44. CCP4 Study Weekend 2017: From Data to Structure
  45. Using PML Scripts to generate PyMOL images
  46. TM-score
  47. Network Representations of Allostery

2016 54

  1. Interesting Antibody Papers.
  2. Addressing the Role of Conformational Diversity in Protein Structure Prediction
  3. Transgenic Mosquitoes
  4. Interesting Antibody Papers
  5. The Emerging Disorder-Function Paradigm
  6. How to Calculate PLIFs Using RDKit and PLIP
  7. End of an era?
  8. Start2Fold: A database of protein folding and stability data
  9. A global genetic interaction network maps a wiring diagram of cellular function
  10. Viewing 3D molecules interactively in Jupyter iPython notebooks
  11. SMEs in Research
  12. Plotting and storing a 3D network in R
  13. Is contacts-based protein-protein affinity prediction the way forward?
  14. Physical-chemical property predictors as command line tools
  15. Counting Threads
  16. The Protein World
  17. A beginner’s guide to Rosetta
  18. What happens to the Human Immune Repertoire over time?
  19. Processing large files using python: part duex
  20. Processing large files using python
  21. Colour wisely…
  22. Seventh Joint Sheffield Conference on Cheminformatics Part 1 (#ShefChem16)
  23. Tracked changes in LaTeX
  24. Rational Design of Antibody Protease Inhibitors
  25. Quantifying dispersion under varying instrument precision
  26. Improving the precision of local community detection
  27. Conformational Variation of Protein Loops
  28. “Identifying Allosteric Hotspots with Dynamics”: Using molecular simulation to find critical sites for the functional motions in proteins
  29. Comp Chem Kitchen
  30. RDKit User Group Meeting 2016
  31. Advances in Conformer Generation: ETKDG and ETDG
  32. Structure prediction through sequence physical properties
  33. Visualising Biological Data, Pt. 2
  34. Convergent affinity maturation.
  35. Is “fragment-based” still the way forward in template-free protein structure prediction?
  36. Journal Club: “Discriminative Chemical Patterns: Automatic and Interactive Design”
  37. Do we need the constant regions of Antibodies and T-cell receptors in molecular simulations?
  38. Visualising Biological Data, Pt. 1
  39. Journal Club: Comments on Three X-ray Crystal Structure Papers
  40. Network Comparison
  41. Strachey Lecture – “Artificial Intelligence and the Future” by Dr. Demis Hassabis
  42. Community structure in multilayer networks
  43. Drawing Custom Unrooted Trees from Sequence Alignments
  44. Inserting functional proteins in an antibody
  45. Identifying basic building blocks/motifs of networks
  46. Novelty in Drug Discovery
  47. Designing antibodies targeting disordered epitopes
  48. New toys for OPIG
  49. Loop Model Selection
  50. Network Pharmacology
  51. Co-translational insertion and folding of membrane proteins
  52. Network Hubs
  53. Next generation sequencing of paired heavy and light chain sequences
  54. We can model everything, right…?

2015 41

  1. Isoform-resolved protein interaction networks and poker
  2. Molecular Diversity and Drug Discovery
  3. Racing along transcripts: Correlating ribosome profiling and protein structure.
  4. Journal Club: Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo
  5. A designed conformational shift to control protein binding specificity
  6. Short project: “Network Approach to Identifying the Mode of Action of Environmental Changes in Yeast”
  7. Journal Club: Accessing Protein Conformational Ensembles using RT X-ray Crystallography
  8. SABS short project presentation: Multilayer Networks
  9. ISMB wrap-up (it was coming, we insist…!)
  10. ERC starting grant mock interview
  11. Molecular Dynamics of Antibody CDRs
  12. Slow and steady improvements in the prediction of one-dimensional protein features
  13. Predicted protein contacts: is it the solution to (de novo) protein structure prediction?
  14. Modelling antibodies, from Sequence, to Structure…
  15. Le tour d’OPIG 2015
  16. Using B factors to assess flexibility
  17. Journal Club: Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion
  18. Protein loops – why do we care?
  19. Antibody binding site re-design
  20. GO annotations: Warning – secondary IDs!
  21. Ways to compare networks
  22. Diseases exploiting the Power of Networks
  23. Journal Club: AbDesign. An algorithm for combinatorial backbone design guided by natural conformations and sequences
  24. 5 Thoughts For… Comparing Crystallographic Datasets
  25. From 300 superpositions/sec to 6,000,000 superpositions/sec. A Python to C story
  26. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
  27. Clustering Algorithms
  28. Investigating structural mechanisms with customised Natural Moves
  29. SAS-5 assists in building centrioles of nematode worms Caenorhabditis elegans
  30. Investigating GPCR kink variation
  31. Submitting your thesis!
  32. Journal Club: The Origin of CDR H3 Structural Diversity
  33. Hierachical Natural Move Monte Carlo using MOSAICS
  34. A new method to improve network topological similarity search: applied to fold recognition
  35. What does a farm look like? – Evaluating Community Detection Methods
  36. Graphical User Interface for MOSAICS as a PyMOL plugin — PymoSAICS
  37. A topology-based distance measure for network data
  38. Building accurate models of membrane protein structures
  39. Hypotheses and Perspectives onto de novo protein structure prediction
  40. Improving the accuracy of CDR-H3 structure prediction
  41. Predicting Antibody Affinities – Progress?

2014 45

  1. Looking for a null model of PPI ego-networks
  2. OOMMPPAA: A tool to aid directed synthesis by the combined analysis of activity and structural data
  3. How do we measure translation speed?
  4. How to (not) perform a Molecular Dynamics simulation study
  5. Research Talk: Ligand Fitting in X-ray Crystallography
  6. Augmented Modelling with Natural Move Monte Carlo Simulations
  7. Finding Communities in Networks: Link Clustering and the Affiliation Graph Model
  8. ECCB 2014 (Strasbourg)
  9. A program to aid primary protein structure determination -1962 style.
  10. The origins of exponential random graph models
  11. Modeling of Protein Interaction Networks
  12. PLOS Comp Bio’s front page!
  13. HHSearch
  14. Dssp
  15. Loopy LaTeX
  16. OPIG goes Punting!
  17. 3Dsig and ISMB 2014 (Boston)
  18. Antibody CDR-H3 Modelling with Prime
  19. Sampling Conformations of Antibodies using MOSAICS
  20. Computational Antibody Affinity Maturation
  21. Le Tour de Farce v2.0
  22. Antibody modeling via AMA II and RosettaAntibody
  23. Journal club (Bernhard Knapp): MMPBSA Binding Free Energy Calculations
  24. Natural Move Monte Carlo: Sampling Collective Motions in Proteins
  25. Protein Folding: Man vs Machine
  26. de novo Protein Structure Prediction software: an elegant “monkey with a typewriter”
  27. MAMMOTH: a case study in protein structure alignment
  28. Distance matrix clustering
  29. Freezing python code
  30. OPIG Algorithm Club Problem #1: The 3n+1 problem
  31. Introduction to the protein folding problem
  32. Quick Standalone BLAST Setup for Ubuntu Linux
  33. Journal Club: Statistical Quality Indicators for Electron Density Maps
  34. Structural Biology Module @ the DTC
  35. Journal Club: Native contacts in protein folding
  36. Journal Club: Random Coordinate Descent
  37. Kinetic Modelling of Co-translational Protein Folding (Journal Club)
  38. Expanding Anfinsen’s Principle (Journal Club)
  39. Activity cliffs
  40. Stepwise Assembly For Protein Loop Prediction
  41. CAPRI, pyDock and the state of protein-protein docking.
  42. Journal Club: A Novel Insight into Gene Ontology Semantic Similarity
  43. OPIC Christmas party 16th of January 2014
  44. Journal Club: Ligand placement based on prior structures: the guided ligand-replacement method
  45. Journal Club: Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

2013 69

  1. Journal Club: Large-scale analysis of somatic hypermutations
  2. Journal Club: Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree
  3. Efficient discovery of overlapping communities in massive networks
  4. How many bins?
  5. Annotate Antibody CDR and Framework Residues
  6. Journal club: Half a century of Ramachandran plots
  7. Journal club: NetMHCIIpan-3.0
  8. AH^AH – Alpha Helices Assessed by Humans.
  9. Wilcoxon-Mann-Whitney test and a small sample size
  10. CABS-flex
  11. A Colourblind Guide to Colourful Presentations…
  12. From Protein Interface Recognition to Protein Complex Prediction
  13. Life in Colour – Vim
  14. Conservation of codon optimality
  15. Protein Interaction Networks
  16. Antibody Modelling: CDR-H3 Structure Prediction
  17. Get PDB intermolecular protein contacts and interface residues
  18. Network Analysis
  19. [Publication] Arginine Methylation-Dependent Reader-Writer Interplay Governs Growth Control by E2F-1
  20. Remove all LaTeX generated files
  21. Progress report: Molecular Dynamics simulations of TCRpMHC
  22. Django for scientific applications
  23. What is a kink?
  24. 3035 – OPIG Beer & Cycling
  25. A very long introductory post about protein structure prediction
  26. ISMB/ECCB Conference 2013 (Berlin)
  27. Every Protein needs a Friend – Community Detection in Protein Interaction Networks
  28. [Database] SAbDab – the Structural Antibody Database
  29. Research Talk: High Resolution Antibody Modelling
  30. Citing R packages in your Thesis/Paper/Assignments
  31. [Publication] Cloud computing in Molecular Modelling – a topical perspective
  32. Making Protein-Protein Interfaces Look (decently) Good
  33. Building an Antibody Benchmark Set
  34. Evolutionary fold space preferences
  35. Antimicrobial Drug Discovery Conference (Madrid)
  36. [Publication] Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and Structure
  37. Standardize a PDB
  38. And the Oscar goes to …
  39. Protein kinases, the PIM story
  40. Inside Memoir: MP-T aligns membrane proteins
  41. [Publication] Memoir: template-based structure prediction for membrane proteins
  42. Free food!
  43. Journalclub: Molecular Dynamics simulations of TCRpMHC
  44. Journal Club: Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
  45. Constrain a PDB to particular chains
  46. Making small molecules look good in PyMOL
  47. Viewing ligands in twilight electron density
  48. GPGPUs for bioinformatics
  49. PredyFlexy – Predicting Protein Flexibility
  50. Journal club: Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature
  51. Good looking proteins for your publication(s)
  52. A javascript function to validate FASTA sequences
  53. Journal Club: Can Linear Progamming (LP) be useful to us?
  54. Journal Club: Protein structure model refinement using fragment-guided MD
  55. aRrrrgh! or how to apply a fitted model to new data
  56. On being cool: arrows on an R plot
  57. Journal club: Improving the selectivity of antimicrobial peptides
  58. A free, sweet, valid HTML4 “Site Maintenance” page
  59. Recognizing pitfalls in Virtual Screening: A critical review
  60. How to install RDKit on Ubuntu 12.04 / 12.10 / 13.04 / 13.10 / 14.04 / 14.10 (with InChI support)
  61. Journal Club: A mathematical framework for structure comparison
  62. How to make a custom latex bibliography style
  63. Conservation of kinks in membrane proteins
  64. Journal Club: The complexity of Binding
  65. How to make environment variables persist in your web app (Apache2)
  66. Journal club: Antibody-protein docking using asymmetric statistical potential
  67. Anatomy of a blog post
  68. Journal club: Principles for designing ideal protein structures
  69. Talk: Membrane Protein 3D Structure Prediction & Loop Modelling in X-ray Crystallography