Patrick McCabe
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View article: Data-Driven Generation of Conformational Ensembles and Ternary Complexes for PROTAC and Other Chimera Systems
Data-Driven Generation of Conformational Ensembles and Ternary Complexes for PROTAC and Other Chimera Systems Open
We present the protolysis-targeting chimera (PROTAC) Conformer Generator, a fast and knowledge-based tool for generating robust conformational ensembles of PROTACs and other chimeric degraders. The modeling protocol integrates conformer ge…
View article: What has scripting ever done for us? The CSD Python application programming interface (API)
What has scripting ever done for us? The CSD Python application programming interface (API) Open
Since its first release in 2016, the Cambridge Structural Database Python application programming interface (CSD Python API) has seen steady uptake within the community that the Cambridge Crystallographic Data Centre serves. This article r…
View article: Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters Open
Three-dimensional (3D) deep molecular generative models offer the advantage of goal-directed generation based on 3D-dependent properties, such as binding affinity for structure-based design within binding pockets. Traditional benchmarks cr…
View article: Deep generative models for 3D molecular structure
Deep generative models for 3D molecular structure Open
Deep generative models have gained recent popularity for chemical design. Many of these models have historically operated in 2D space; however, more recently explicit 3D molecular generative models have become of interest, which are the to…
View article: <i>Mercury 4.0</i>: from visualization to analysis, design and prediction
<i>Mercury 4.0</i>: from visualization to analysis, design and prediction Open
The program Mercury , developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography an…
View article: Crystal structure prediction of flexible pharmaceutical-like molecules: density functional tight-binding as an intermediate optimisation method and for free energy estimation
Crystal structure prediction of flexible pharmaceutical-like molecules: density functional tight-binding as an intermediate optimisation method and for free energy estimation Open
Periodic DFTB3-D3 calculations allow the refinement of molecular conformations within crystal structures and estimates of phonons for flexible pharmaceutical molecules.
View article: Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules
Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules Open
Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information fr…
View article: Near/far-side angular decompositions of Legendre polynomials using the amplitude-phase method
Near/far-side angular decompositions of Legendre polynomials using the amplitude-phase method Open
A decomposition of Legendre polynomials into propagating angular waves is derived with the aid of an amplitude-phase method. This decomposition is compared with the ’Nussenzveig/Fuller’ so called near/far-side decomposition of Legendre pol…
View article: Generation of crystal structure landscapes using known crystal structures
Generation of crystal structure landscapes using known crystal structures Open
We analyze the energy landscape of the 6 th crystal structure prediction blind test targets with various ab inito and semiempirical methodologies.A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical met…
View article: Report on the sixth blind test of organic crystal structure prediction methods
Report on the sixth blind test of organic crystal structure prediction methods Open
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexi…
View article: Generation of crystal structures using known crystal structures as analogues
Generation of crystal structures using known crystal structures as analogues Open
This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for s…
View article: Sixth CCDC Blind Test: Calculated Crystal Structures
Sixth CCDC Blind Test: Calculated Crystal Structures Open
A set of calculated crystal structures for target XXV in the CCDC's sixth blind test of organic crystal-structure prediction methods, corresponding to list 1 of submission 2. These structures are freely available from the CCDC and include …
View article: Sixth CCDC Blind Test: Calculated Crystal Structures
Sixth CCDC Blind Test: Calculated Crystal Structures Open
A set of calculated crystal structures for target XXII in the CCDC's sixth blind test of organic crystal-structure prediction methods, corresponding to list 1 of submission 2. These structures are freely available from the CCDC and include…
View article: Sixth CCDC Blind Test: Calculated Crystal Structures
Sixth CCDC Blind Test: Calculated Crystal Structures Open
A set of calculated crystal structures for target XXIII in the CCDC's sixth blind test of organic crystal-structure prediction methods, corresponding to list 1 of submission 2. These structures are freely available from the CCDC and includ…
View article: Sixth CCDC Blind Test: Calculated Crystal Structures
Sixth CCDC Blind Test: Calculated Crystal Structures Open
A set of calculated crystal structures for target XXVI in the CCDC's sixth blind test of organic crystal-structure prediction methods, corresponding to list 1 of submission 2. These structures are freely available from the CCDC and include…