Deep learning in protein structural modeling and design
Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and
powerful computational resources, impacting many fields, including protein structural …
powerful computational resources, impacting many fields, including protein structural …
Asymmetric catalysis mediated by synthetic peptides, version 2.0: expansion of scope and mechanisms
Low molecular weight synthetic peptides have been demonstrated to be effective catalysts
for an increasingly wide array of asymmetric transformations. In many cases, these peptide …
for an increasingly wide array of asymmetric transformations. In many cases, these peptide …
[PDF][PDF] Towards automated crystallographic structure refinement with phenix. refine
PV Afonine, RW Grosse-Kunstleve… - … Section D: Biological …, 2012 - journals.iucr.org
phenix. refine is a program within the PHENIX package that supports crystallographic
structure refinement against experimental data with a wide range of upper resolution limits …
structure refinement against experimental data with a wide range of upper resolution limits …
ACPYPE-Antechamber python parser interface
Abstract Background ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper
script around the ANTECHAMBER software that simplifies the generation of small molecule …
script around the ANTECHAMBER software that simplifies the generation of small molecule …
Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel
Abstract α-Synuclein (aSyn) fibrillar polymorphs have distinct in vitro and in vivo seeding
activities, contributing differently to synucleinopathies. Despite numerous prior attempts, how …
activities, contributing differently to synucleinopathies. Despite numerous prior attempts, how …
An automated force field topology builder (ATB) and repository: version 1.0
The Automated force field Topology Builder (ATB, http://compbio. biosci. uq. edu. au/atb) is a
Web-accessible server that can provide topologies and parameters for a wide range of …
Web-accessible server that can provide topologies and parameters for a wide range of …
[HTML][HTML] Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes
Inflammasomes elicit host defense inside cells by activating caspase-1 for cytokine
maturation and cell death. AIM2 and NLRP3 are representative sensor proteins in two major …
maturation and cell death. AIM2 and NLRP3 are representative sensor proteins in two major …
Distance-based protein folding powered by deep learning
J Xu - Proceedings of the National Academy of Sciences, 2019 - National Acad Sciences
Direct coupling analysis (DCA) for protein folding has made very good progress, but it is not
effective for proteins that lack many sequence homologs, even coupled with time-consuming …
effective for proteins that lack many sequence homologs, even coupled with time-consuming …
Current status of the AMOEBA polarizable force field
Molecular force fields have been approaching a generational transition over the past several
years, moving away from well-established and well-tuned, but intrinsically limited, fixed point …
years, moving away from well-established and well-tuned, but intrinsically limited, fixed point …
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
ARP/wARP is a software suite to build macromolecular models in X-ray crystallography
electron density maps. Structural genomics initiatives and the study of complex …
electron density maps. Structural genomics initiatives and the study of complex …