Wang H, Sun M, Xie L, Liu D, Zhang G
Comput Struct Biotechnol J. 2025; 27:478-487.
PMID: 39916698
PMC: 11799971.
DOI: 10.1016/j.csbj.2025.01.017.
Wang Y, Zhou Y, Khan F
Int J Mol Sci. 2025; 25(24.
PMID: 39769245
PMC: 11677904.
DOI: 10.3390/ijms252413482.
Gholizadeh A, Amjad-Iranagh S, Halladj R
ACS Omega. 2024; 9(39):40433-40445.
PMID: 39372004
PMC: 11447843.
DOI: 10.1021/acsomega.4c02551.
Nguyen B, Singh V, Afrin S, Singh P, Pekala M, Ahmed Y
Commun Biol. 2024; 7(1):905.
PMID: 39068302
PMC: 11283564.
DOI: 10.1038/s42003-024-06588-6.
Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J
Elife. 2024; 13.
PMID: 38941236
PMC: 11213569.
DOI: 10.7554/eLife.94836.
Molecular surface descriptors to predict antibody developability: sensitivity to parameters, structure models, and conformational sampling.
Park E, Izadi S
MAbs. 2024; 16(1):2362788.
PMID: 38853585
PMC: 11168226.
DOI: 10.1080/19420862.2024.2362788.
Atomic resolution structure of full-length human insulin fibrils.
Suladze S, Sarkar R, Rodina N, Bokvist K, Krewinkel M, Scheps D
Proc Natl Acad Sci U S A. 2024; 121(23):e2401458121.
PMID: 38809711
PMC: 11161806.
DOI: 10.1073/pnas.2401458121.
Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.
Cao X, Hummel M, Wang Y, Simmerling C, Coutsias E
J Chem Theory Comput. 2024; 20(11):4456-4468.
PMID: 38780181
PMC: 11530138.
DOI: 10.1021/acs.jctc.3c01366.
Exotic self-assembly of hard spheres in a morphometric solvent.
Spirandelli I, Coles R, Friesecke G, Evans M
Proc Natl Acad Sci U S A. 2024; 121(15):e2314959121.
PMID: 38573965
PMC: 11009619.
DOI: 10.1073/pnas.2314959121.
Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis.
Nguyen B, Singh V, Afrin S, Singh P, Pekala M, Ahmed Y
bioRxiv. 2024; .
PMID: 38496656
PMC: 10942412.
DOI: 10.1101/2024.03.08.582936.
Conformational Space of the Translocation Domain of Botulinum Toxin: Atomistic Modeling and Mesoscopic Description of the Coiled-Coil Helix Bundle.
Delort A, Cottone G, Malliavin T, Muller M
Int J Mol Sci. 2024; 25(5).
PMID: 38473729
PMC: 10931374.
DOI: 10.3390/ijms25052481.
Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models.
Tsai C, Lin C, Ye G, Wu S, Yao P, Lin C
ACS Omega. 2024; 9(8):9357-9374.
PMID: 38434814
PMC: 10905719.
DOI: 10.1021/acsomega.3c08676.
Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs.
Cao X, Hummel M, Wang Y, Simmerling C, Coutsias E
ArXiv. 2024; .
PMID: 38313200
PMC: 10836080.
Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy.
Nguyen B, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y
Nat Commun. 2024; 15(1):581.
PMID: 38233397
PMC: 10794703.
DOI: 10.1038/s41467-024-44820-3.
Fibril structures of TFG protein mutants validate the identification of TFG as a disease-related amyloid protein by the IMPAcT method.
Rosenberg G, Abskharon R, Boyer D, Ge P, Sawaya M, Eisenberg D
PNAS Nexus. 2023; 2(12):pgad402.
PMID: 38077690
PMC: 10703350.
DOI: 10.1093/pnasnexus/pgad402.
Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2.
Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J
bioRxiv. 2023; .
PMID: 38045241
PMC: 10690151.
DOI: 10.1101/2023.11.21.568093.
Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core.
Richards L, Flores M, Zink S, Schibrowsky N, Sawaya M, Rodriguez J
Structure. 2023; 31(11):1386-1393.e3.
PMID: 37657439
PMC: 11456264.
DOI: 10.1016/j.str.2023.08.007.
Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach.
Abdul-Khalek N, Wimmer R, Overgaard M, Gregersen Echers S
Comput Struct Biotechnol J. 2023; 21:3715-3727.
PMID: 37560124
PMC: 10407266.
DOI: 10.1016/j.csbj.2023.07.027.
CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach.
Durojaye O, Ejaz U, Uzoeto H, Fadahunsi A, Opabunmi A, Ekpo D
Amino Acids. 2023; 55(12):1745-1764.
PMID: 37500789
DOI: 10.1007/s00726-023-03304-2.
Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories.
Hsieh Y, Delarue M, Orland H, Koehl P
Viruses. 2023; 15(6).
PMID: 37376665
PMC: 10300701.
DOI: 10.3390/v15061366.