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Article ; Online: The Phenix-AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix.

Poon, Billy K / Terwilliger, Thomas C / Adams, Paul D

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 5, Page(s) e4992

Abstract: Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo-electron microscopy data. The Phenix software suite has AlphaFold ... ...

Abstract	Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo-electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model-building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix-AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.
MeSH term(s)	Software ; Models, Molecular ; Proteins/chemistry ; Protein Conformation ; Protein Folding ; Machine Learning ; Internet
Chemical Substances	Proteins
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4992
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Article ; Online: Targeting K-Ras Mutations Show Promise Towards Ending Ras's "Undruggable" Era.

Adams, Paul D / Muhoza, Djamali

Protein and peptide letters

2022 Volume 29, Issue 12, Page(s) 1007–1015

Abstract: It has almost been 40 years since the Ras proteins were discovered as the first human oncogenes. They remain among the most important genes for regulating mammalian cell growth and are involved in more than a quarter of human cancers. Out of 167 members ... ...

Abstract	It has almost been 40 years since the Ras proteins were discovered as the first human oncogenes. They remain among the most important genes for regulating mammalian cell growth and are involved in more than a quarter of human cancers. Out of 167 members of the Ras superfamily, KRas mutations are the most abundant in human cancers. Particularly, the K-Ras G12C mutations are known to be involved in pancreatic, colon and lung cancers as well as leukemias. Though progress has been made, approaches targeting Ras proteins for therapeutic purposes remain challenging. No drugs treating Ras-related cancers are currently on the market. However, there is now renewed interest in the Ras area, and newer approaches have highlighted the targeting of several types of tumors and treating cancer patients. This review will summarize recent K-Ras drug candidates and approaches in the preclinical, clinical and post-clinical pipelines that show promise for targeting and reducing Ras-related tumors. Macromolecules such as mRNA vaccines, siRNA, and T-cell receptors that target Ras will also be discussed. The newer molecules and the recent approaches to be discussed suggest that the "undruggable" era of Ras proteins could be coming to an end.
MeSH term(s)	Humans ; Mutation ; Neoplasms/drug therapy ; Neoplasms/genetics ; Oncogenes ; ras Proteins/genetics ; Antineoplastic Agents/pharmacology
Chemical Substances	ras Proteins (EC 3.6.5.2) ; Antineoplastic Agents
Language	English
Publishing date	2022-10-05
Publishing country	Netherlands
Document type	Review ; Journal Article
ZDB-ID	1280776-x
ISSN	1875-5305 ; 0929-8665
ISSN (online)	1875-5305
ISSN	0929-8665
DOI	10.2174/0929866529666221003124202
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Article ; Online: Accounting for nonuniformity of bulk-solvent: A mosaic model.

Afonine, Pavel V / Adams, Paul D / Sobolev, Oleg V / Urzhumtsev, Alexandre G

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 3, Page(s) e4909

Abstract: A flat mask-based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model is occupied by the solvent. The ... ...

Abstract	A flat mask-based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model is occupied by the solvent. The properties of this solvent are assumed to be exactly the same across the whole volume of the unit cell. While this is a reasonable approximation in practice, there are a number of scenarios where this model becomes suboptimal. In this work, we enumerate several of these scenarios and describe a new generalized approach to modeling the bulk-solvent which we refer to as mosaic bulk-solvent model. The mosaic bulk-solvent model allows nonuniform features of the solvent in the crystal to be accounted for in a computationally efficient way. It is implemented in the computational crystallography toolbox and the Phenix software.
MeSH term(s)	Solvents/chemistry ; Crystallography, X-Ray ; Software ; Macromolecular Substances/chemistry
Chemical Substances	Solvents ; Macromolecular Substances
Language	English
Publishing date	2024-02-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4909
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Article ; Online: Efficient structure-factor modeling for crystals with multiple components.

Afonine, Pavel V / Adams, Paul D / Urzhumtsev, Alexandre G

Acta crystallographica. Section A, Foundations and advances

2023 Volume 79, Issue Pt 4, Page(s) 345–352

Abstract: Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by ... ...

Abstract	Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by an atomic model alone, i.e. using point scatterers. Indeed, entities such as disordered (bulk) solvent, semi-ordered solvent (e.g. lipid belts in membrane proteins, ligands, ion channels) and disordered polymer loops require other types of modeling than a collection of individual atoms. This results in the model structure factors containing multiple contributions. Most macromolecular applications assume two-component structure factors: one component arising from the atomic model and the second one describing the bulk solvent. A more accurate and detailed modeling of the disordered regions of the crystal will naturally require more than two components in the structure factors, which presents algorithmic and computational challenges. Here an efficient solution of this problem is proposed. All algorithms described in this work have been implemented in the computational crystallography toolbox (CCTBX) and are also available within Phenix software. These algorithms are rather general and do not use any assumptions about molecule type or size nor about those of its components.
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020844-3
ISSN	2053-2733 ; 1600-5724 ; 0108-7673
ISSN (online)	2053-2733 ; 1600-5724
ISSN	0108-7673
DOI	10.1107/S205327332300356X
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Article ; Online: Post-Anesthesia Cognitive Dysfunction in Mice Is Associated with an Age-Related Increase in Neuronal Intracellular [Ca

Uryash, Arkady / Mijares, Alfredo / Lopez, Carlos E / Adams, Jose A / Allen, Paul D / Lopez, Jose R

Cells

2024 Volume 13, Issue 3

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	Mice ; Humans ; Animals ; Middle Aged ; Aged ; Isoflurane/adverse effects ; Anesthetics, Inhalation/toxicity ; Neuroprotective Agents/therapeutic use ; Calpain ; Reactive Oxygen Species/adverse effects ; Dantrolene/pharmacology ; Cognitive Dysfunction/drug therapy ; Cognitive Dysfunction/chemically induced ; Mice, Inbred C57BL ; Anesthesia ; Neurons
Chemical Substances	Isoflurane (CYS9AKD70P) ; Anesthetics, Inhalation ; Neuroprotective Agents ; Calpain (EC 3.4.22.-) ; Reactive Oxygen Species ; Dantrolene (F64QU97QCR)
Language	English
Publishing date	2024-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells13030264
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Article ; Online: In situ ligand restraints from quantum-mechanical methods.

Liebschner, Dorothee / Moriarty, Nigel W / Poon, Billy K / Adams, Paul D

Acta crystallographica. Section D, Structural biology

2023 Volume 79, Issue Pt 2, Page(s) 100–110

Abstract: In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of ... ...

Abstract	In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ, thus accounting for the influence of the macromolecule on the local energy minima of the ligand. The optimized ligand geometry is used to generate target values for geometric restraints during the crystallographic refinement. As demonstrated using a sample of >2330 ligand instances in >1700 protein-ligand models, QMR restraints generally result in lower deviations from the target stereochemistry compared with conventionally generated restraints. In particular, the QMR approach provides accurate torsion restraints for ligands and other entities.
MeSH term(s)	Protein Conformation ; Ligands ; Models, Molecular ; Software ; Crystallography, X-Ray ; Proteins/chemistry
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2023-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798323000025
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Article ; Online: An Engineered Laccase from

Pham, Le Thanh Mai / Deng, Kai / Choudhary, Hemant / Northen, Trent R / Singer, Steven W / Adams, Paul D / Simmons, Blake A / Sale, Kenneth L

Biomolecules

2024 Volume 14, Issue 3

Abstract: Laccases from white-rot fungi catalyze lignin depolymerization, a critical first step to upgrading lignin to valuable biodiesel fuels and chemicals. In this study, a wildtype laccase from the ... ...

Abstract	Laccases from white-rot fungi catalyze lignin depolymerization, a critical first step to upgrading lignin to valuable biodiesel fuels and chemicals. In this study, a wildtype laccase from the basidiomycete
MeSH term(s)	Lignin/chemistry ; Laccase/metabolism ; Basidiomycota/metabolism ; Carbohydrates ; Cellulases ; Sugars ; Ethers
Chemical Substances	lignocellulose (11132-73-3) ; Lignin (9005-53-2) ; Laccase (EC 1.10.3.2) ; Carbohydrates ; Cellulases (EC 3.2.1.-) ; Sugars ; Ethers
Language	English
Publishing date	2024-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom14030324
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Article ; Online: Improved joint X-ray and neutron refinement procedure in Phenix.

Liebschner, Dorothee / Afonine, Pavel V / Poon, Billy K / Moriarty, Nigel W / Adams, Paul D

Acta crystallographica. Section D, Structural biology

2023 Volume 79, Issue Pt 12, Page(s) 1079–1093

Abstract: ... from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and ... is more complex as it usually requires additional parameters to describe the H (and D) atoms ...

Abstract	Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.
MeSH term(s)	X-Rays ; X-Ray Diffraction ; Crystallography ; Neutron Diffraction/methods ; Neutrons ; Crystallography, X-Ray
Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798323008914
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Article ; Online: Iron-sulfur clusters have no right angles.

Moriarty, Nigel W / Adams, Paul D

Acta crystallographica. Section D, Structural biology

2019 Volume 75, Issue Pt 1, Page(s) 16–20

Abstract: Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the ... ...

Abstract	Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe
MeSH term(s)	Crystallography, X-Ray/methods ; Cysteine ; Data Mining ; Databases, Protein ; Iron-Sulfur Proteins/chemistry
Chemical Substances	Iron-Sulfur Proteins ; Cysteine (K848JZ4886)
Language	English
Publishing date	2019-01-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020492-9
ISSN	2059-7983 ; 1399-0047 ; 0907-4449
ISSN (online)	2059-7983 ; 1399-0047
ISSN	0907-4449
DOI	10.1107/S205979831801519X
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Article ; Online: Overall protein structure quality assessment using hydrogen-bonding parameters.

Afonine, Pavel V / Sobolev, Oleg V / Moriarty, Nigel W / Terwilliger, Thomas C / Adams, Paul D

Acta crystallographica. Section D, Structural biology

2023 Volume 79, Issue Pt 8, Page(s) 684–693

Abstract: Atomic model refinement at low resolution is often a challenging task. This is mostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is ... ...

Abstract	Atomic model refinement at low resolution is often a challenging task. This is mostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is geometrically meaningful, additional information needs to be used such as restraints on Ramachandran plot distributions or residue side-chain rotameric states. However, using Ramachandran plots or rotameric states as refinement targets diminishes the validating power of these tools. Therefore, finding additional model-validation criteria that are not used or are difficult to use as refinement goals is desirable. Hydrogen bonds are one of the important noncovalent interactions that shape and maintain protein structure. These interactions can be characterized by a specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for quality-filtered high-resolution models of proteins from the Protein Data Bank shows that they have a distinct and a conserved distribution. Here, it is demonstrated how this information can be used for atomic model validation.
MeSH term(s)	Hydrogen Bonding ; Crystallography, X-Ray ; Models, Molecular ; Proteins/chemistry ; Hydrogen ; Protein Conformation
Chemical Substances	Proteins ; Hydrogen (7YNJ3PO35Z)
Language	English
Publishing date	2023-07-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798323005077
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