Paul Bond

Computational Structural Biologist

University of York

Structural Biology Software Development X-ray Crystallography Data Analysis Machine Learning

Projects

ModelCraft

Automated model-building pipeline for X-ray crystallography and cryo-EM

JTSA

Interactively analyse thermal shift (DSF) data by fitting sigmoid curves

V-Lab

Virtual simulations of undergraduate analytical laboratory experiments

Fprime

Compare anomalous scattering factors (f' and f") for different elements

Cluedo Solver

Input guesses and responses to work out the true suspect, weapon and location

Focus

A simple Pomodoro timer to help focus on tasks for 25 minute periods

Colour Evolution

Introduction to evolutionary algorithms using an evolving grid of random colours

Workshops

Coot Workshop
A two-part workshop to introduce interactive model building in Coot

RNA Model Building Workshop
An introduction to the model building tools available in CCP4 for nucleic acid structures

CCP4 Molecular Graphics Tutorial
A tutorial covering most of the basic features of CCP4mg

Publications

NucleoFind: a deep-learning network for interpreting nucleic acid electron density
J Dialpuri, J Agirre, K Cowtan, P Bond
Nucleic Acids Res., 52, e84 (2024)

The CCP4 suite: integrative software for macromolecular crystallography
J Agirre, et al.
Acta Cryst. D, 79, 449 (2023)

ModelCraft: an advanced automated model-building pipeline using Buccaneer
P Bond, K Cowtan
Acta Cryst. D, 78, 1090 (2022)

Shift-field refinement of macromolecular atomic models
K Cowtan, S Metcalfe, P Bond
Acta Cryst. D, 76, 1192 (2020)

Predicting protein model correctness in Coot using machine learning
P Bond, K Wilson, K Cowtan
Acta Cryst. D, 76, 713 (2020)

See the full list on Google Scholar

Presentations

Model Building and Density Modification
Overview of the Cowtan group programs for density modification and model building in CCP4: Parrot, Buccaneer, Nautilus and ModelCraft.

Automatic Model Building (CCP4 / CCP-EM)
Overview of the automated model-building programs available in CCP4 and CCP-EM.