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References from Investigating the effects of missense mutations on the dual Ras/Rap activation mechanism of SYNGAP1 using molecular modelling. Local targets link to admitted publications; unresolved targets remain external evidence.
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10.1016/1074-5521(95)90101-9 · 1995 · External reference
SYNGAP1 mutations: clinical, genetic, and pathophysiological features
10.1016/j.ijdevneu.2019.08.003 · 2019 · External reference
Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras
10.1038/nsb0997-686 · 1997 · External reference
Structural fingerprints of the Ras-GTPase activating proteins neurofibromin and p120GAP
10.1016/s0022-2836(03)00514-x · 2003 · External reference
Unresolved reference
2022 · External reference
The Rosetta all-atom energy function for macromolecular modeling and design
10.1021/acs.jctc.7b00125 · 2017 · External reference
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1
2024 · External reference
SynGAP regulates synaptic plasticity and cognition independently of its catalytic activity
2024 · External reference
Rapid dispersion of SynGAP from synaptic spines triggers AMPA receptor insertion and spine enlargement during LTP
10.1016/j.neuron.2014.12.023 · 2015 · External reference
10.1101/2023.08.06.552111
10.1101/2023.08.06.552111 · External reference
Flex ddG: Rosetta Ensemble-based estimation of changes in protein-protein binding affinity upon mutation
10.1021/acs.jpcb.7b11367 · 2018 · External reference
The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6
2022 · External reference
Cutting the brakes on ras-cytoplasmic gaps as targets of inactivation in cancer
2020 · External reference
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10.1063/1.448118 · 1984 · External reference
10.1016/s0304-419x(02)00082-3
10.1016/s0304-419x(02)00082-3 · External reference
Mechanism-based redesign of GAP to activate oncogenic Ras
10.1021/jacs.3c04330 · 2023 · External reference
GEFs and GAPs: critical elements in the control of small G proteins
2007 · External reference
10.1073/pnas.2427288122
10.1073/pnas.2427288122 · External reference
10.1016/j.csbj.2018.01.002 · 2018 · Admitted local publication
Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1
10.1038/ng.2646 · 2013 · External reference
Unresolved reference
2023 · External reference
AmberTools
10.1021/acs.jcim.3c01153 · 2023 · External reference
PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta
10.1093/bioinformatics/btq007 · 2010 · External reference
Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C integrase-Dolutegravir binding
2020 · External reference
The GTPase-activating protein Rap1GAP uses a catalytic asparagine
10.1038/nature02505 · 2004 · External reference
An update on the tumor-suppressive functions of the RasGAP protein DAB2IP with focus on therapeutic implications. Cell death and differentiation. Springer
2024 · External reference
Phosphorylation promotes binding affinity of rap-Raf complex by allosteric modulation of switch loop dynamics
2018 · External reference
Transition state structures and the roles of catalytic residues in GAP-facilitated GTPase of Ras as elucidated by 18O kinetic isotope effects
10.1021/bi802359b · 2009 · External reference
Unresolved reference
External reference
Rosettascripts: A scripting language interface to the Rosetta macromolecular modeling suite
2011 · External reference
Independent metrics for protein backbone and side-chain flexibility: time scales and effects of ligand binding
10.1021/ct500633u · 2015 · External reference
Twenty years of syngap research: from synapses to cognition. Journal of neuroscience. Society for
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Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal
2013 · External reference
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10.1101/2020.09.30.320069 · External reference
Roadmap to advance therapeutics for SYNGAP1-related disorder: a patient organization perspective from SynGAP research fund
2025 · External reference
Unresolved reference
2011 · External reference
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
10.1016/s0022-2836(02)00442-4 · 2002 · External reference
Mutations in SYNGAP1 in autosomal nonsyndromic mental retardation
10.1056/nejmoa0805392 · 2009 · External reference
Structure of the TSC2 GAP domain: mechanistic insight into catalysis and pathogenic mutations
10.1016/j.str.2020.05.008 · 2020 · External reference
The NCI genomic data commons
10.1038/s41588-021-00791-5 · 2021 · External reference
The biology of IQGAP proteins: beyond the cytoskeleton
10.15252/embr.201439834 · 2015 · External reference
Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method
10.1002/minf.201100135 · 2012 · External reference
Investigating the volume and diversity of data needed for generalizable antibody–antigen ΔΔG prediction
10.1038/s43588-025-00823-8 · 2025 · External reference
VMD: Visual molecular dynamics
10.1016/0263-7855(96)00018-5 · 1996 · External reference
Building water models: A different approach
10.1021/jz501780a · 2014 · External reference
SYNGAP1: mind the gap
10.3389/fncel.2016.00032 · 2016 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Key roles of C2/GAP domains in SYNGAP1-related pathophysiology
10.1016/j.celrep.2024.114733 · 2024 · External reference
Unresolved reference
External reference
GTPase catalysis by Ras and other G-proteins: insights from substrate directed SuperImposition
10.1016/s0022-2836(03)00847-7 · 2003 · External reference
SynGAP-MUPP1-CaMKII synaptic complexes regulate p38 MAP kinase activity and NMDA receptor- dependent synaptic AMPA receptor potentiation
10.1016/j.neuron.2004.08.003 · 2004 · External reference
GAP1 family members constitute bifunctional Ras and rap GTPase-activating proteins
10.1074/jbc.m512802200 · 2006 · External reference
The ability of GAP1 IP4BP to function as a Rap1 GTPase-activating protein (GAP) requires its Ras GAP-related domain and an arginine finger rather than an asparagine thumb
10.1128/mcb.00427-09 · 2009 · External reference
Unresolved reference
1992 · External reference
Binding of Ca2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study
10.1016/j.str.2021.05.011 · 2021 · External reference
Biological phosphoryl-transfer reactions: understanding mechanism and catalysis
10.1146/annurev-biochem-060409-092741 · 2011 · External reference
Rosetta3: An object-oriented software suite for the simulation and design of macromolecules
10.1016/b978-0-12-381270-4.00019-6 · 2011 · External reference
BODIL: a molecular modeling environment for structure-function analysis and drug design
10.1007/s10822-004-3752-4 · 2004 · External reference
Macromolecular modeling and design in Rosetta: recent methods and frameworks
10.1038/s41592-020-0848-2 · 2020 · External reference
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water
10.1021/jp505875v · 2015 · External reference
Tumor suppression of Ras GTPase-activating protein RASA5 through antagonizing Ras signaling perturbation in carcinomas
10.1016/j.isci.2019.10.007 · 2019 · External reference
Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide
10.1002/bip.360320508 · 1992 · External reference
The role of ras-associated protein 1 (Rap1) in cancer: bad actor or good player? Biomedicines
2020 · External reference
A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants
10.1093/brain/awaa051 · 2020 · External reference
The role of Gln 61 in HRas GTP hydrolysis: A quantum mechanics/molecular mechanics study
10.1016/j.bpj.2011.11.4005 · 2012 · External reference
The RasGAP gene, RASAL2, is a tumor and metastasis suppressor
10.1016/j.ccr.2013.08.004 · 2013 · External reference
Multi-parametric analysis of 57 SYNGAP1 variants reveal impacts on GTPase signaling, localization, and protein stability
10.1016/j.ajhg.2020.11.011 · 2021 · External reference
Unresolved reference
External reference
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10.7717/peerj.1674 · External reference
Spa-1 (Sipa1) and rap signaling in leukemia and cancer metastasis
10.1111/j.1349-7006.2008.01011.x · 2009 · External reference
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
10.1002/jcc.540130805 · 1992 · External reference
The Ras GTPase-activating protein Rasal3 supports survival of naive T cells supports survival of naive T cells
2015 · External reference
Mechanistic insights into GTP hydrolysis by the RhoA protein: catalytic impact of glutamine Tautomerism
10.1021/acscatal.5c00719 · 2025 · External reference
Glutamine Tautomerization drives RhoGAP-aided GTP hydrolysis in small rho GTPases
10.1021/jacs.6c06153 · 2026 · External reference
GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation
2023 · External reference
The C2 domain augments Ras GTPase-activating protein catalytic activity
2025 · External reference
Unresolved reference
2025 · External reference
The C2 domain of SynGAP is essential for stimulation of the rap GTPase reaction
10.1038/embor.2008.20 · 2008 · External reference
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
10.1093/protein/gzp030 · 2009 · External reference
Dab2IP regulates neuronal positioning, rap1 activity and integrin signaling in the developing cortex
10.1159/000369092 · 2015 · External reference
KRAS G13D sensitivity to neurofibromin-mediated GTP hydrolysis
10.1073/pnas.1908353116 · 2019 · External reference
The semaphorin 3A receptor may directly regulate the activity of small GTPases
10.1016/s0014-5793(00)02240-7 · 2000 · External reference
RASAL3, a novel hematopoietic RasGAP protein, regulates the number and functions of NKT cells
10.1002/eji.201444977 · 2015 · External reference
Comparative protein modelling by satisfaction of spatial restraints
10.1006/jmbi.1993.1626 · 1993 · External reference
Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability
2023 · External reference
Database resources of the national center for biotechnology information
10.1093/nar/gkab1112 · 2022 · External reference
Unresolved reference
2019 · External reference
The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants
1979 · External reference
The PyMOL molecular graphics system
2019 · External reference
Unresolved reference
External reference
Prediction of water and metal binding sites and their affinities by using the fold-X force field
10.1073/pnas.0501980102 · 2005 · External reference
The FoldX web server: An online force field
2005 · External reference
The rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues
10.1038/emboj.2008.30 · 2008 · External reference
The importance of two conserved arginine residues for catalysis by the Ras GTPase-activating protein, neurofibromin
10.1074/jbc.273.16.9480 · 1998 · External reference
Downregulation of Rap1Gap: A switch from DCIS to invasive breast carcinoma via ERK/MAPK activation
10.1016/j.neo.2018.07.002 · 2018 · External reference
Unresolved reference
2019 · External reference
COSMIC: a curated database of somatic variants and clinical data for cancer
10.1093/nar/gkad986 · 2024 · External reference
RosettaDDGPrediction for high-throughput mutational scans: from stability to binding
2023 · External reference
Unravelling the mechanism of dual-specificity GAPs
10.1038/emboj.2010.20 · 2010 · External reference
How Ras works: structure of a rap-Raf complex
10.1016/s0969-2126(01)00198-8 · 1995 · External reference
Unresolved reference
2019 · External reference
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
10.1021/acs.jctc.9b00591 · 2020 · External reference
A graphical interface for the FoldX forcefield
10.1093/bioinformatics/btr254 · 2011 · External reference
Unresolved reference
External reference
Phosphorylation of synaptic GTPase-activating protein (synGAP) by polo-like kinase (Plk2) alters the ratio of its GAP activity toward HRas, Rap1 and Rap2 GTPases
10.1016/j.bbrc.2018.07.087 · 2018 · External reference
Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward ras and rap GTPases
10.1074/jbc.m114.614420 · 2015 · External reference
Plexins are GTPase-activating proteins for rap and are activated by induced dimerization
2012 · External reference
Structural basis for activation and non-canonical catalysis of the rap GTPase activating protein domain of plexin
2013 · External reference
Allostery in its many disguises: from theory to applications
2019 · External reference
Unresolved reference
2017 · External reference
Clinical and behavioural features of SYNGAP1-related intellectual disability: a parent and caregiver description
2022 · External reference
Overexpression of SYNGAP1 suppresses the proliferation of rectal adenocarcinoma via Wnt/β-catenin signaling pathway. Discover
2024 · External reference
Structural insights into the SPRED1-Neurofibromin-KRAS complex and disruption of SPRED1-Neurofibromin interaction by oncogenic EGFR
2020 · External reference
The RASAL2 variant promotes aberrant RAS signaling and resistance to anti-EGFR therapy in colorectal cancer
2025 · External reference
Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides
10.1631/jzus.b1500106 · 2015 · External reference
Phase transition in postsynaptic densities underlies formation of synaptic complexes and synaptic plasticity
10.1016/j.cell.2016.07.008 · 2016 · External reference
The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism
10.1093/jmcb/mjt044 · 2014 · External reference
Roles of Rap1 signaling in tumor cell migration and invasion. Cancer biology and medicine
2017 · External reference
RASAL2 plays inconsistent roles in different cancers
10.3389/fonc.2019.01235 · 2019 · External reference
Ras and rap control AMPA receptor trafficking during synaptic plasticity
10.1016/s0092-8674(02)00897-8 · 2002 · External reference
