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An iterative knowledge‐based scoring function for protein–protein recognition
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
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Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
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Use of pair potentials across protein interfaces in screening predicted docked complexes
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Examination of shape complementarity in docking of Unbound proteins
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BiGGER: A new (soft) docking algorithm for predicting protein interactions
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Residue frequencies and pairing preferences at protein-protein interfaces
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An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
inferredcites →https://doi.org/10.1002/jcc.20505openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
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An all atom force field for simulations of proteins and nucleic acids
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Potential of mean force for protein–protein interaction studies
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Docking unbound proteins using shape complementarity, desolvation, and electrostatics
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
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A novel shape complementarity scoring function for protein‐protein docking
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10460openalex-snapshot
RDOCK: Refinement of rigid‐body protein docking predictions
inferredcites →https://doi.org/10.1002/prot.1070openalex-snapshot
Protein docking using a genetic algorithm
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.20576openalex-snapshot
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
inferredcites →https://doi.org/10.1002/prot.20859openalex-snapshot
Optimal design of protein docking potentials: Efficiency and limitations
inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot
PIPER: An FFT‐based protein docking program with pairwise potentials
inferredcites →https://doi.org/10.1002/prot.21214openalex-snapshot
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21406openalex-snapshot
Protein docking using surface matching and supervised machine learning
inferredcites →https://doi.org/10.1002/prot.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21495openalex-snapshot
FireDock: Fast interaction refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.21498openalex-snapshot
A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
inferredcites →https://doi.org/10.1006/jmbi.1996.0175openalex-snapshot
Statistical Potentials Extracted From Protein Structures: How Accurate Are They?
inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/0-306-46883-2_7openalex-snapshot
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
inferredcites →https://doi.org/10.1007/978-0-387-68372-0_3openalex-snapshot
Knowledge-Based Energy Functions for Computational Studies of Proteins
inferredcites →https://doi.org/10.1007/978-0-387-68825-1openalex-snapshot
Computational Methods for Protein Structure Prediction and Modeling
inferredcites →https://doi.org/10.1016/0022-2836(78)90302-9openalex-snapshot
Computer analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0022-2836(91)80222-gopenalex-snapshot
Protein docking and complementarity
inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot
“Soft docking”: Matching of molecular surface cubes
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
inferredcites →https://doi.org/10.1016/s0006-3495(03)74997-2openalex-snapshot
Development of Unified Statistical Potentials Describing Protein-Protein Interactions
inferredcites →https://doi.org/10.1016/s0022-2836(03)00670-3openalex-snapshot
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot
Calculation of conformational ensembles from potentials of mena force
inferredcites →https://doi.org/10.1016/s0022-2836(95)80063-8openalex-snapshot
A geometry-based suite of moleculardocking processes
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1016/s0959-440x(97)80029-2openalex-snapshot
Empirical potentials and functions for protein folding and binding
inferredcites →https://doi.org/10.1016/s1074-5521(96)90256-2openalex-snapshot
Predicting the structure of protein complexes: a step in the right direction
inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot
A new force field for molecular mechanical simulation of nucleic acids and proteins
inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/ma00145a039openalex-snapshot
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
inferredcites →https://doi.org/10.1021/ma60054a013openalex-snapshot
Medium- and Long-Range Interaction Parameters between Amino Acids for Predicting Three-Dimensional Structures of Proteins
inferredcites →https://doi.org/10.1023/a:1008729005958openalex-snapshot
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1073/pnas.93.21.11628openalex-snapshot
An iterative method for extracting energy-like quantities from protein structures.
inferredcites →https://doi.org/10.1093/bioinformatics/4.1.35openalex-snapshot
A software tool for finding locally optimal alignments in protein and nucleic acid sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btl447openalex-snapshot
D ockground resource for studying protein–protein interfaces
inferredcites →https://doi.org/10.1093/comjnl/7.4.308openalex-snapshot
A Simplex Method for Function Minimization
inferredcites →https://doi.org/10.1093/nar/gki481openalex-snapshot
PatchDock and SymmDock: servers for rigid and symmetric docking
inferredcites →https://doi.org/10.1093/nar/gkl768openalex-snapshot
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures
inferredcites →https://doi.org/10.1093/protein/14.2.105openalex-snapshot
Protein docking using continuum electrostatics and geometric fit
inferredcites →https://doi.org/10.1093/protein/7.1.39openalex-snapshot
Molecular surface recognition by a computer vision-based technique
inferredcites →https://doi.org/10.1103/physreve.68.011202openalex-snapshot
Determination of the interaction potential from the pair distribution function: An inverse Monte Carlo technique
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Geometric Hashing: A General And Efficient Model-based Recognition Scheme
inferredcites →https://doi.org/10.1110/ps.0239303openalex-snapshot
Protein–protein docking with a reduced protein model accounting for side‐chain flexibility
inferredcites →https://doi.org/10.1110/ps.03348304openalex-snapshot
An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state
inferredcites →https://doi.org/10.1110/ps.03484604openalex-snapshot
A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications
inferredcites →https://doi.org/10.1110/ps.062501507openalex-snapshot
Efficient molecular docking of NMR structures: Application to HIV‐1 protease
inferredcites →https://doi.org/10.1110/ps.26002openalex-snapshot
Electrostatics in protein–protein docking
inferredcites →https://doi.org/10.1110/ps.2830102openalex-snapshot
Protein–protein docking with multiple residue conformations and residue substitutions
inferredcites →https://doi.org/10.1529/biophysj.106.092122openalex-snapshot
Poisson-Boltzmann Calculations of Nonspecific Salt Effects on Protein-Protein Binding Free Energies
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Predicting Molecular Interactions in silico: II. Protein-Protein and Protein- Drug Docking
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SurfPro-NN: A 3D point cloud neural network for the scoring of protein–protein docking models based on surfaces features and protein language models
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A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2023.107660openalex-snapshot
ComDock: A novel approach for protein-protein docking with an efficient fusing strategy
inferred← citeshttps://doi.org/10.1016/j.dci.2025.105348openalex-snapshot
The evolution and functional characterization of transcription factors E2Fs in lamprey, Lethenteron reissneri
inferred← citeshttps://doi.org/10.1016/j.drudis.2014.02.005openalex-snapshot
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
inferred← citeshttps://doi.org/10.1016/j.drudis.2015.03.007openalex-snapshot
Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking
inferred← citeshttps://doi.org/10.1016/j.drudis.2025.104382openalex-snapshot
Computational methods for modeling protein–protein interactions in the AI era: Current status and future directions
inferred← citeshttps://doi.org/10.1016/j.expneurol.2026.115747openalex-snapshot
Nrf2 modulates the IRF7–SLC31A1 axis to suppress neuronal cuproptosis after traumatic brain injury
inferred← citeshttps://doi.org/10.1016/j.gendis.2025.101665openalex-snapshot
Unraveling the role of the WIPF1/ACTN4 complex in podosome formation of human placental EVTs: Insights into recurrent spontaneous abortion
inferred← citeshttps://doi.org/10.1016/j.gene.2019.03.040openalex-snapshot
Bioinformatics analysis of evolutionary characteristics and biochemical structure of FGF5 Gene in sheep
inferred← citeshttps://doi.org/10.1016/j.heliyon.2020.e05739openalex-snapshot
Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e34721openalex-snapshot
Development of a novel multi-epitope vaccine for brucellosis prevention
inferred← citeshttps://doi.org/10.1016/j.heliyon.2025.e42478openalex-snapshot
In silico evaluation of missense SNPs in cancer-associated Cystatin A protein and their potential to disrupt Cathepsin B interaction
inferred← citeshttps://doi.org/10.1016/j.ifset.2023.103367openalex-snapshot
Identification of peptides from defatted wheat germ proteins with dual functionality: Emulsifying activity and anti-adhesive activity against Helicobacter pylori
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.136166openalex-snapshot
A potent antimicrobial glycolipopeptide GLIP and its promising combined antimicrobial effect
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.137061openalex-snapshot
P-type pilus PapG protein elicits toll-like receptor 2-mediated immune activation during cancer immunotherapy
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.137270openalex-snapshot
Deciphering the mechanism underlying poor aqueous solubility of extracted quinoa proteins
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.147060openalex-snapshot
Characterization of BpLPMO10 from Bacillus paralicheniformis: A bi-functional AA10 LPMO with chitin-preferential activity and strong exo-enzyme synergy
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.148269openalex-snapshot
La3+ and Dy3+ hexaaza macrocycles revisited: Enhanced stabilization of G-quadruplex DNA - spectroscopic and in silico studies
inferred← citeshttps://doi.org/10.1016/j.imu.2023.101257openalex-snapshot
Prediction of HCV E2 association with the host-cell chaperone, GRP78
inferred← citeshttps://doi.org/10.1016/j.insi.2026.100383openalex-snapshot
Immunobioinformatic approaches for development of multi-epitope vaccine against mpox targeting attachment, entry-fusion and immune evasion proteins of mpox virus
inferred← citeshttps://doi.org/10.1016/j.isci.2023.107498openalex-snapshot
Developing a peptide to disrupt cohesin head domain interactions
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107438openalex-snapshot
Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties
inferred← citeshttps://doi.org/10.1016/j.jff.2023.105590openalex-snapshot
Butyrylcholinesterase inhibitory activity of peptides identified from yellow field pea (Pisum sativum) enzymatic protein hydrolysates
inferred← citeshttps://doi.org/10.1016/j.jmb.2024.168540openalex-snapshot
CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes
inferred← citeshttps://doi.org/10.1016/j.jmgm.2008.12.005openalex-snapshot
Molecular modeling of the heterodimer of human CFTR’s nucleotide-binding domains using a protein–protein docking approach
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.04.001openalex-snapshot
Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein–protein docking results
inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.06.011openalex-snapshot
Shape complementarity at protein interfaces via global docking optimisation
inferred← citeshttps://doi.org/10.1016/j.jmgm.2025.109150openalex-snapshot
Comprehensive computational modeling and interactions mechanisms of GIPR homodimerization
inferred← citeshttps://doi.org/10.1016/j.jpcs.2025.112693openalex-snapshot
Co-crystallization of nonlinear optical diisopropylammonium pentaborate monohydrate: Structural, mechanical, thermal attributes, DFT precision modeling and docking studies
inferred← citeshttps://doi.org/10.1016/j.jpi.2023.100190openalex-snapshot
Bioinformatics evaluation of anticancer properties of GP63 protein-derived peptides on MMP2 protein of melanoma cancer
inferred← citeshttps://doi.org/10.1016/j.microc.2026.117205openalex-snapshot
Evaluation and grading of binding capability of target proteins to oligonucleotide libraries: A critical factor to drive effective aptamer screening
inferred← citeshttps://doi.org/10.1016/j.molliq.2024.125491openalex-snapshot
Design and synthesis of new benzoxazole derivatives and study of their interactions with a G4 model by UV spectroscopy and in silico methods
inferred← citeshttps://doi.org/10.1016/j.mtbio.2025.102384openalex-snapshot
Microenvironment-responsive size-adaptive nanoparticles: hyaluronidase/acid/NIR light activation for deep-penetration trimodal therapy
inferred← citeshttps://doi.org/10.1016/j.nantod.2025.102821openalex-snapshot
Nanogels confined superactive LOx-CPO for TME-responsive enzyme-gene therapy
inferred← citeshttps://doi.org/10.1016/j.phrs.2024.107376openalex-snapshot
Diarylpropionitrile-stimulated ERβ nuclear accumulation promotes MyoD-induced muscle regeneration in mdx mice by interacting with FOXO3A
inferred← citeshttps://doi.org/10.1016/j.phymed.2026.158174openalex-snapshot
Spermidine alleviates sepsis-induced cardiomyopathy by improving mitochondrial quality and quantity via a Metallothionein 1–dependent antioxidant pathway
inferred← citeshttps://doi.org/10.1016/j.phymed.2026.158722openalex-snapshot
Targeting the 14-3-3θ protein with indole-3-propionic acid restores PINK1/Parkin mediated mitophagy and suppresses endothelial PANoptosis in atherosclerosis
inferred← citeshttps://doi.org/10.1016/j.poly.2025.117794openalex-snapshot
Design, synthesis, and biological investigation of N-heterocyclic carbene –silver complexes for catalytic multicomponent coupling reactions
inferred← citeshttps://doi.org/10.1016/j.sbi.2010.02.001openalex-snapshot
Accounting for conformational changes during protein–protein docking
inferred← citeshttps://doi.org/10.1016/j.sbi.2020.05.017openalex-snapshot
Computational structure modeling for diverse categories of macromolecular interactions
inferred← citeshttps://doi.org/10.1016/j.softx.2020.100462openalex-snapshot
iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines
inferred← citeshttps://doi.org/10.1016/j.str.2016.07.021openalex-snapshot
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction
inferred← citeshttps://doi.org/10.1016/j.talanta.2025.129054openalex-snapshot
Truncated PNA-functionalized porous silicon biosensor for low-cost and early detection of troponin T in myocardial infarction
inferred← citeshttps://doi.org/10.1016/j.virusres.2022.198769openalex-snapshot
Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides
inferred← citeshttps://doi.org/10.1016/j.ymeth.2016.03.004openalex-snapshot
Structural computational modeling of RNA aptamers
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot
Mean-Force Scoring Functions for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.biochem.3c00562openalex-snapshot
Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae
inferred← citeshttps://doi.org/10.1021/acs.bioconjchem.3c00200openalex-snapshot
Tryptophan-PNA gc Conjugates Self-Assemble to Form Fibers
inferred← citeshttps://doi.org/10.1021/acs.jafc.4c03761openalex-snapshot
QPH-FR: A Novel Quinoa Peptide Enhances Chemosensitivity by Targeting Leucine-Rich Repeat-Containing G Protein-Coupled Receptor 5 in Colorectal Cancer
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00058openalex-snapshot
Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00974openalex-snapshot
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00198openalex-snapshot
Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein–Protein Docking, Molecular Dynamics, and MM-GBSA Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00836openalex-snapshot
Predicting Protein–Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01483openalex-snapshot
Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01961openalex-snapshot
Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00339openalex-snapshot
Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00372openalex-snapshot
Knowledge of Native Protein–Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00601openalex-snapshot
New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00142openalex-snapshot
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00565openalex-snapshot
How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways?
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00057openalex-snapshot
Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00445openalex-snapshot
CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00687openalex-snapshot
GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01990openalex-snapshot
Evaluation of protein–RNA Docking Web Servers for Template-Free Docking and Comparison with the AlphaFold Server
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00557openalex-snapshot
Docking Flexible Cyclic Peptides with AutoDock CrankPep
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c01826openalex-snapshot
Introduction of a Glycine Linker Connecting the Heavy and Light Chains in Synthetic Cardosin B-Derived Rennet Changes the Specificity of Subpocket S3′
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04421openalex-snapshot
Iterative Knowledge-Based Scoring Function for Protein–Ligand Interactions by Considering Binding Affinity Information
inferred← citeshttps://doi.org/10.1021/acs.nanolett.6c01869openalex-snapshot
Development of a Nanoscale Protein–Protein Mapping of PDE4 Interface-Disrupting Peptides
inferred← citeshttps://doi.org/10.1021/acschembio.1c00866openalex-snapshot
Efficient Enzymatic Incorporation of Dehydroalanine Based on SAMDI-Assisted Identification of Optimized Tags for OspF/SpvC
inferred← citeshttps://doi.org/10.1021/acsnano.2c10249openalex-snapshot
Dual-Mechanism Glycolipidpeptide with High Antimicrobial Activity, Immunomodulatory Activity, and Potential Application for Combined Antibacterial Therapy
inferred← citeshttps://doi.org/10.1021/ci100353eopenalex-snapshot
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking
inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferred← citeshttps://doi.org/10.1021/ci500647fopenalex-snapshot
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
inferred← citeshttps://doi.org/10.1021/ci9002987openalex-snapshot
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ct3007925openalex-snapshot
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties
inferred← citeshttps://doi.org/10.1038/nprot.2016.169openalex-snapshot
The ClusPro web server for protein–protein docking
inferred← citeshttps://doi.org/10.1038/s41396-023-01544-4openalex-snapshot
Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments
inferred← citeshttps://doi.org/10.1038/s41401-026-01937-zopenalex-snapshot
TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction
inferred← citeshttps://doi.org/10.1038/s41419-024-06569-xopenalex-snapshot
OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway
inferred← citeshttps://doi.org/10.1038/s41419-026-08750-wopenalex-snapshot
TFAM promotes mitochondrial division by increasing mitochondrial Sirt3
inferred← citeshttps://doi.org/10.1038/s41420-025-02727-yopenalex-snapshot
CERS6 promotes esophageal squamous cell carcinoma proliferation by increasing the stability of RPN1
inferred← citeshttps://doi.org/10.1038/s41467-021-23923-1openalex-snapshot
IL-6 regulates autophagy and chemotherapy resistance by promoting BECN1 phosphorylation
inferred← citeshttps://doi.org/10.1038/s41467-022-32370-5openalex-snapshot
Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT
inferred← citeshttps://doi.org/10.1038/s41467-023-40426-3openalex-snapshot
Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes
inferred← citeshttps://doi.org/10.1038/s41467-025-63256-xopenalex-snapshot
Multiple myeloma associated long non-coding RNA PLUM confers chemoresistance by enhancing PRC2 mediated UPR pathway activation
inferred← citeshttps://doi.org/10.1038/s41596-020-0312-xopenalex-snapshot
The HDOCK server for integrated protein–protein docking
inferred← citeshttps://doi.org/10.1038/s41598-020-80900-2openalex-snapshot
Classification and prediction of protein–protein interaction interface using machine learning algorithm
inferred← citeshttps://doi.org/10.1038/s41598-022-13622-2openalex-snapshot
Fibronectin containing alternatively spliced extra domain A interacts at the central and c-terminal domain of Toll-like receptor-4
inferred← citeshttps://doi.org/10.1038/s41598-024-57117-8openalex-snapshot
Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of NaV1.2 and NaV1.6
inferred← citeshttps://doi.org/10.1038/s41598-025-89342-0openalex-snapshot
Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches
inferred← citeshttps://doi.org/10.1038/s42256-025-01136-1openalex-snapshot
An interaction-derived graph learning framework for scoring protein–peptide complexes
inferred← citeshttps://doi.org/10.1038/s44319-026-00746-zopenalex-snapshot
YAP1 and QSER1 are key modulators of embryonic signaling pathways in the mammalian epiblast
inferred← citeshttps://doi.org/10.1038/s44321-025-00256-wopenalex-snapshot
NRF2 modulates WNT signaling pathway to enhance photodynamic therapy resistance in oral leukoplakia
inferred← citeshttps://doi.org/10.1039/9781849735049-00219openalex-snapshot
Coarse-grain Protein Models
inferred← citeshttps://doi.org/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferred← citeshttps://doi.org/10.1039/d2cb00207hopenalex-snapshot
Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction
inferred← citeshttps://doi.org/10.1039/d3cp04980aopenalex-snapshot
Evaluation of DNA–protein complex structures using the deep learning method
inferred← citeshttps://doi.org/10.1039/d5nj04117aopenalex-snapshot
Substituted NHC–PEPPSI–Pd( ii ) complexes: synthesis, characterization, DFT calculations and catalytic application in thiazole C–H arylation
inferred← citeshttps://doi.org/10.1063/1.3615722openalex-snapshot
Energy design for protein-protein interactions
inferred← citeshttps://doi.org/10.1073/pnas.1010124107openalex-snapshot
Ion sensing in the RCK1 domain of BK channels
inferred← citeshttps://doi.org/10.1080/07391102.2022.2118167openalex-snapshot
Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae : a molecular docking and simulation study
inferred← citeshttps://doi.org/10.1080/07391102.2022.2160817openalex-snapshot
Dronabinol as an answer to flavivirus infections: an in-silico investigation
inferred← citeshttps://doi.org/10.1080/07391102.2023.2192797openalex-snapshot
Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods
inferred← citeshttps://doi.org/10.1080/07391102.2024.2331100openalex-snapshot
MD investigation on the differences in the dynamic interactions between the specific ligand azamulin and two CYP3A isoforms, 3A4 and 3A5
inferred← citeshttps://doi.org/10.1088/1361-6633/ac3800openalex-snapshot
Physics of biomolecular recognition and conformational dynamics
inferred← citeshttps://doi.org/10.1088/1572-9494/ac7042openalex-snapshot
cgRNASP-CN: a minimal coarse-grained representation-based statistical potential for RNA 3D structure evaluation
inferred← citeshttps://doi.org/10.1088/1674-1056/27/2/020503openalex-snapshot
Optimizing the atom types of proteins through iterative knowledge-based potentials
inferred← citeshttps://doi.org/10.1088/1674-1056/abc0d6openalex-snapshot
Statistical potentials for 3D structure evaluation: From proteins to RNAs*
inferred← citeshttps://doi.org/10.1088/1674-1056/abc14eopenalex-snapshot
Protein–protein docking with interface residue restraints*
inferred← citeshttps://doi.org/10.1089/nat.2011.0313openalex-snapshot
Rational Truncation of an RNA Aptamer to Prostate-Specific Membrane Antigen Using Computational Structural Modeling
inferred← citeshttps://doi.org/10.1093/bib/bbac330openalex-snapshot
Studying protein–protein interaction through side-chain modeling method OPUS-Mut
inferred← citeshttps://doi.org/10.1093/bioadv/vbad011openalex-snapshot
G-RANK: an equivariant graph neural network for the scoring of protein–protein docking models
inferred← citeshttps://doi.org/10.1093/bioadv/vbad070openalex-snapshot
PIQLE: protein–protein interface quality estimation by deep graph learning of multimeric interaction geometries
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa207openalex-snapshot
A knowledge-based scoring function to assess quaternary associations of proteins
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac120openalex-snapshot
TRScore: a 3D RepVGG-based scoring method for ranking protein docking models
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac486openalex-snapshot
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad203openalex-snapshot
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15
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