Research graph
References from Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins. Local targets link to admitted publications; unresolved targets remain external evidence.
Serpin structure, mechanism, and function
10.1021/cr010170+ · 2002 · External reference
Serpins: Finely Balanced Conformational Traps
10.1080/15216540213825 · 2002 · External reference
Serpin structure, function and dysfunction
10.1111/j.1538-7836.2011.04360.x · 2011 · External reference
Serpinopathies and the conformational dementias
10.1038/nrg907 · 2002 · External reference
What can Drosophila tell us about serpins, thrombosis and dementia?
10.1002/bies.10407 · 2004 · External reference
The role of conformational change in serpin structure and function
10.1002/bies.950150705 · 1993 · External reference
Antithrombin. A bloody important serpin
1997 · External reference
The genetics of antithrombin
10.1016/j.thromres.2018.07.008 · 2018 · External reference
Factors with conformational effects on haemostatic serpins: Implications in thrombosis
10.1160/th07-02-0152 · 2007 · External reference
Principles that Govern the Folding of Protein Chains
1973 · External reference
Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble
10.1038/s41598-022-13714-z · 2022 · External reference
Highly accurate protein structure prediction with AlphaFold
2021 · External reference
It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures
10.1038/d41586-020-03348-4 · 2020 · External reference
Critical assessment of methods of protein structure prediction (CASP)—Round XIII.
10.1002/prot.25823 · 2019 · External reference
Improved protein structure prediction using potentials from deep learning
10.1038/s41586-019-1923-7 · 2020 · External reference
Critical Assessment of Techniques for Protein Structure Prediction, Fourteenth round.
2020 · External reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · 2021 · External reference
Unresolved reference
2021 · External reference
Can AlphaFold2 predict the impact of missense mutations on structure?
10.1038/s41594-021-00714-2 · 2022 · External reference
Using AlphaFold to predict the impact of single mutations on protein stability and function.
2023 · External reference
Long-timescale molecular dynamics simulations of protein structure and function
10.1016/j.sbi.2009.03.004 · 2009 · External reference
Dynamics of folded proteins
10.1038/267585a0 · 1977 · External reference
Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein.
10.1021/acscentsci.0c01056 · 2020 · External reference
Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations.
10.1038/s41598-020-69322-2 · 2020 · External reference
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome.
10.1038/s41557-021-00707-0 · 2021 · External reference
High levels of latent antithrombin in plasma from patients with antithrombin deficiency
10.1160/th16-11-0866 · 2017 · External reference
Antithrombin p.Thr147Ala: The First Founder Mutation in People of African Origin Responsible for Inherited Antithrombin Deficiency
10.1055/s-0040-1716531 · 2021 · External reference
Detection of conformational transformation of antithrombin in blood with crossed immunoelectrophoresis: new application for a classical method
10.1016/s0022-2143(03)00136-7 · 2003 · External reference
Latent antithrombin and its detection, formation and turnover in the circulation
10.1111/j.1538-7836.2004.01047.x · 2004 · External reference
Antithrombin Murcia (K241E) causing antithrombin deficiency: A possible role for altered glycosylation.
10.3324/haematol.2009.015487 · 2010 · External reference
Antithrombin III Toyama: replacement of arginine-47 by cysteine in hereditary abnormal antithrombin III that lacks heparin-binding ability
10.1073/pnas.81.2.289 · 1984 · External reference
Mutations in the shutter region of antithrombin result in formation of disulfide-linked dimers and severe venous thrombosis
10.1111/j.1538-7836.2004.00749.x · 2004 · External reference
Molecular basis for type 1 antithrombin deficiency: identification of two novel point mutations and evidence for a de novo splice site mutation
10.1182/blood.v84.11.3742.bloodjournal84113742 · 1994 · External reference
Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance
10.1111/j.1538-7836.2012.04839.x · 2012 · External reference
Unresolved reference
2020 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
2022 · External reference
UCSF ChimeraX: Structure visualization for researchers, educators, and developers
10.1002/pro.3943 · 2021 · External reference
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
1996 · External reference
Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).
10.1002/pro.3313 · 2018 · External reference
A molecular dynamics method for simulations in the canonical ensemble
10.1080/00268978400101201 · 1984 · External reference
Unresolved reference
2020 · External reference
Unresolved reference
2020 · External reference
Canonical dynamics: Equilibrium phase-space distributions
10.1103/physreva.31.1695 · 1985 · External reference
Constant pressure molecular dynamics algorithms
10.1063/1.467468 · 1994 · External reference
OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.
10.1021/acs.jctc.8b01026 · 2019 · External reference
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
10.1093/bioinformatics/btt473 · 2013 · External reference
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.
10.1016/j.softx.2015.06.001 · 2015 · External reference
Matplotlib: A 2D Graphics Environment.
10.1109/mcse.2007.55 · 2007 · External reference
VarSome: the human genomic variant search engine. Wren J, editor
10.1093/bioinformatics/bty897 · 2019 · External reference
Unresolved reference
External reference
The role of Arg46 and Arg47 of antithrombin in heparin binding
10.1021/bi990686b · 1999 · External reference
Heparin Activates Antithrombin Anticoagulant Function by Generating New Interaction Sites (Exosites) for Blood Clotting Proteinases.
10.1016/s1050-1738(02)00183-4 · 2002 · External reference
Defects of splicing in antithrombin deficiency
10.1002/rth2.12025 · 2017 · External reference
African derived phytocompounds may interfere with SARS-CoV-2 RNA capping machinery via inhibition of 2′-O-ribose methyltransferase: An in silico perspective
10.1016/j.molstruc.2022.133019 · 2022 · External reference
In vivo effects of hyperthermia on the functional and conformational characteristics of antithrombin
10.1111/j.1538-7836.2007.02479.x · 2007 · External reference
Conformational properties of serine proteinase inhibitors (serpins) confer multiple pathophysiological roles
10.1016/s0925-4439(01)00025-4 · 2001 · External reference
How serpins transport hormones and regulate their release
10.1016/j.semcdb.2016.12.007 · 2017 · External reference
Identification and Characterization of a Misfolded Monomeric Serpin Formed at Physiological Temperature
10.1016/j.jmb.2010.09.007 · 2010 · External reference
Protease inhibitors as models for the study of oxidative folding
10.1089/ars.2010.3456 · 2011 · External reference
Oxidative Stress and Hypoxia: Implications for Plasminogen Activator Inhibitor-1 Expression
10.1089/1523086041361596 · 2004 · External reference
The conformational basis of thrombosis
10.1055/s-0037-1616196 · 2001 · External reference
Thrombosis as a conformational disease
2005 · External reference
The infective polymerization of conformationally unstable antithrombin mutants may play a role in the clinical severity of antithrombin deficiency
10.2119/molmed.2012.00017 · 2012 · External reference
Formation of the Antithrombin Heterodimer In Vivo and the Onset of Thrombosis
10.1182/blood.v94.10.3388.422k20_3388_3396 · 1999 · External reference
Crystallization and Preliminary X-ray Analysis of Human Antithrombin III
10.1006/jmbi.1993.1024 · 1993 · External reference
Crystallization and Preliminary X-ray Diffraction Analysis of Two Conformations of Intact Human Antithrombin
10.1006/jmbi.1993.1676 · 1993 · External reference
Biological implications of a 3 å structure of dimeric antithrombin
10.1016/s0969-2126(00)00028-9 · 1994 · External reference
Unresolved reference
2021 · External reference
Steered Molecular Dynamics Simulation in Rational Drug Design.
10.1021/acs.jcim.8b00261 · 2018 · External reference
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
10.1021/acs.jcim.8b00462 · 2018 · External reference
Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms
10.1021/ar500356n · 2015 · External reference
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. Gorodkin J, editor
10.1093/bioinformatics/btab620 · 2021 · External reference
