Research graph
References from AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Local targets link to admitted publications; unresolved targets remain external evidence.
Generalization of the jarzynski and crooks nonequilibrium work theorems in molecular dynamics simulations
10.1103/physreve.75.050101 · 2007 · External reference
Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning
10.1039/d4cp04579c · 2025 · External reference
Conformational transition and recognition mechanism of eukaryotic riboswitches powered by thiamine pyrophosphate analogues: an elucidation through multiple short molecular dynamics simulations and Markov model
2025 · External reference
10.1021/acs.jcim.1c00844
10.1021/acs.jcim.1c00844 · External reference
Primary vs secondary: directionalized guest coordination in β-Cyclodextrin derivatives
10.1016/j.carbpol.2022.120050 · 2022 · External reference
Dealing with induced fit, conformational selection, and secondary poses in molecular dynamics simulations for reliable free energy predictions
10.1021/acs.jctc.3c00867 · 2023 · External reference
10.1007/s12539-023-00561-3
10.1007/s12539-023-00561-3 · External reference
True dynamics of pillararene Host–Guest binding
10.1021/acs.jctc.4c01361 · 2025 · External reference
From binding to detox: a predictive framework for supramolecular drug capture by cucurbiturils
10.1063/5.0282717 · 2025 · External reference
Diffusion and structure of propylene carbonate–metal salt electrolyte solutions for post-lithium-ion batteries: from experiment to simulation
10.1063/5.0216222 · 2024 · External reference
Structure and dynamics of 5-lipoxygenase and its complexes — a molecular dynamics simulation study
10.1007/s00894-022-05434-y · 2023 · External reference
Altered enthalpy− entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase
10.1021/bi9005896 · 2009 · External reference
Enthalpy—entropy compensation: a phantom phenomenon
10.1007/bf02703768 · 2002 · External reference
10.1016/j.ijbiomac.2025.141454
10.1016/j.ijbiomac.2025.141454 · External reference
10.1093/protein/gzr066
10.1093/protein/gzr066 · External reference
10.1021/acs.jcim.6b00378
10.1021/acs.jcim.6b00378 · External reference
10.1021/ja990935j
10.1021/ja990935j · External reference
Expression patterns, structural features, and roles of SRPX2 in disease pathogenesis
10.1016/j.glycos.2025.100005 · 2025 · External reference
A cancer vaccine based on N-linked sialyl-Tn antigen elicits robust and selective antitumor immunity
10.1016/j.glycos.2025.100006 · 2025 · External reference
Relevance of 3D rotationally equivariant neural networks for predicting Protein-Ligand binding affinities
2025 · External reference
DynamicDTA: drug-target binding affinity prediction using dynamic descriptors and graph representation
2025 · External reference
Protein complex prediction with AlphaFold-Multimer
2022 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
High-resolution de novo structure prediction from primary sequence
2022 · External reference
10.1038/s41592-022-01488-1
10.1038/s41592-022-01488-1 · External reference
10.1038/s41467-022-29394-2
10.1038/s41467-022-29394-2 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
2024 · External reference
AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions
2024 · External reference
10.1371/journal.pone.0161879
10.1371/journal.pone.0161879 · External reference
10.1093/bioinformatics/bts489
10.1093/bioinformatics/bts489 · External reference
10.1006/jmbi.1998.1843
10.1006/jmbi.1998.1843 · External reference
The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces
10.1093/bioinformatics/btg163 · 2003 · External reference
10.1146/annurev.biophys.29.1.291
10.1146/annurev.biophys.29.1.291 · External reference
10.1021/acs.jctc.5b00255
10.1021/acs.jctc.5b00255 · External reference
10.1021/jp8001614
10.1021/jp8001614 · External reference
10.1021/jp902584c
10.1021/jp902584c · External reference
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes
10.1016/0021-9991(77)90098-5 · 1977 · External reference
10.1002/jcc.540130805
10.1002/jcc.540130805 · External reference
Interaction entropy for Protein-Protein binding
10.1063/1.4978893 · 2017 · External reference
10.1002/prot.20033
10.1002/prot.20033 · External reference
10.1002/jcc.10378
10.1002/jcc.10378 · External reference
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
10.1002/(sici)1096-987x(19990130)20:2<217::aid-jcc4>3.0.co;2-a · 1999 · External reference
10.1016/0079-6107(84)90007-5
10.1016/0079-6107(84)90007-5 · External reference
10.1126/science.1096205
10.1126/science.1096205 · External reference
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics
10.1016/j.sbi.2020.08.001 · 2021 · External reference
A benchmark test of High-Throughput atomistic modeling for octa acid Host-guest complexes
2024 · External reference
10.1039/d5cp00895f
10.1039/d5cp00895f · External reference
10.1021/acs.jcim.5c00096
10.1021/acs.jcim.5c00096 · External reference
dMSGB-IE: computational mutational scanning for (de) methylation thermodynamics
10.1063/5.0272070 · 2025 · External reference
Multiscale End-point screening with extended Tight-binding hamiltonians
10.15212/bioi-2025-0071 · 2025 · External reference
10.1021/acs.jcim.6b00734
10.1021/acs.jcim.6b00734 · External reference
10.1021/ct300418h
10.1021/ct300418h · External reference
MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein–protein interactions
10.1093/bib/bbad310 · 2023 · External reference
Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction
10.1038/s41467-024-53583-w · 2024 · External reference
