On the public citation graph

Using AlphaFold and Symmetrical Docking to Predict Protein–Protein Interactions for Exploring Potential Crystallization Conditions

https://doi.org/10.1002/prot.26844
0 signed · 69 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-0134(199708)28:4<494::aid-prot4>3.0.co;2-aopenalex-snapshot
Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
inferredcites →https://doi.org/10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.0.co;2-8openalex-snapshot
Discriminating between homodimeric and monomeric proteins in the crystalline state
inferredcites →https://doi.org/10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.3.co;2-#openalex-snapshot
Discriminating between homodimeric and monomeric proteins in the crystalline state
inferredcites →https://doi.org/10.1002/adma.201304475openalex-snapshot
Methods for SAXS‐Based Structure Determination of Biomolecular Complexes
inferredcites →https://doi.org/10.1002/cmdc.202000565openalex-snapshot
Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses
inferredcites →https://doi.org/10.1002/jcc.23952openalex-snapshot
Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro
inferredcites →https://doi.org/10.1002/pro.4898openalex-snapshot
Systematic enhancement of protein crystallization efficiency by bulk lysine‐to‐arginine ( KR ) substitution
inferredcites →https://doi.org/10.1002/pro.5167openalex-snapshot
Benchmarking reverse docking through AlphaFold2 human proteome
inferredcites →https://doi.org/10.1002/pro.5560061021openalex-snapshot
Protein—protein crystal‐packing contacts
inferredcites →https://doi.org/10.1002/prot.20954openalex-snapshot
A combinatorial score to distinguish biological and nonbiological protein–protein interfaces
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.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.26171openalex-snapshot
High‐accuracy protein structure prediction in CASP14
inferredcites →https://doi.org/10.1002/prot.340230413openalex-snapshot
Protein–protein interaction at crystal contacts
inferredcites →https://doi.org/10.1007/978-1-4939-7000-1_4openalex-snapshot
The “Sticky Patch” Model of Crystallization and Modification of Proteins for Enhanced Crystallizability
inferredcites →https://doi.org/10.1007/978-981-10-8612-0_66openalex-snapshot
A Design Framework for Instrumenting Analytic Provenance for Problem-Solving Tasks
inferredcites →https://doi.org/10.1007/s00018-007-7451-xopenalex-snapshot
The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
inferredcites →https://doi.org/10.1016/j.bbapap.2012.12.003openalex-snapshot
Utilization of protein intrinsic disorder knowledge in structural proteomics
inferredcites →https://doi.org/10.1016/j.cell.2014.10.051openalex-snapshot
A Glimpse of Structural Biology through X-Ray Crystallography
inferredcites →https://doi.org/10.1016/j.jmb.2003.12.073openalex-snapshot
A Dissection of Specific and Non-specific Protein–Protein Interfaces
inferredcites →https://doi.org/10.1016/j.jmb.2005.05.066openalex-snapshot
The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure
inferredcites →https://doi.org/10.1016/j.jmb.2021.167127openalex-snapshot
Integrative Structural Biology in the Era of Accurate Structure Prediction
inferredcites →https://doi.org/10.1016/j.jsb.2012.05.013openalex-snapshot
High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative
inferredcites →https://doi.org/10.1016/j.pbiomolbio.2004.07.008openalex-snapshot
Protein crystallization: virtual screening and optimization
inferredcites →https://doi.org/10.1016/j.str.2004.03.008openalex-snapshot
Rational Protein Crystallization by Mutational Surface Engineering
inferredcites →https://doi.org/10.1016/j.ymeth.2004.03.019openalex-snapshot
Introduction to protein crystallization
inferredcites →https://doi.org/10.1016/s0021-9258(18)67888-3openalex-snapshot
The Amino Acid Sequence of Egg White Lysozyme
inferredcites →https://doi.org/10.1016/s1047-8477(03)00041-8openalex-snapshot
The protein as a variable in protein crystallization
inferredcites →https://doi.org/10.1021/acs.jcim.6b00163openalex-snapshot
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation
inferredcites →https://doi.org/10.1021/jacs.0c10697openalex-snapshot
Facile Fabrication of Protein–Macrocycle Frameworks
inferredcites →https://doi.org/10.1038/nsb1295-1062openalex-snapshot
Why protein crystals favour some space-groups over others
inferredcites →https://doi.org/10.1038/nsb1297-973openalex-snapshot
Specific versus non-specific contacts in protein crystals
inferredcites →https://doi.org/10.1038/s41563-023-01683-1openalex-snapshot
Accurate computational design of three-dimensional protein crystals
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-snapshot
Highly accurate protein structure prediction with AlphaFold
inferredcites →https://doi.org/10.1038/s41586-024-07487-wopenalex-snapshot
Accurate structure prediction of biomolecular interactions with AlphaFold 3
inferredcites →https://doi.org/10.1038/s41592-023-02087-4openalex-snapshot
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination
inferredcites →https://doi.org/10.1038/s41598-018-26497-zopenalex-snapshot
A Novel Geometry-Based Approach to Infer Protein Interface Similarity
inferredcites →https://doi.org/10.1038/s42003-023-05610-7openalex-snapshot
Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning
inferredcites →https://doi.org/10.1039/c3sm52175copenalex-snapshot
Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study
inferredcites →https://doi.org/10.1093/bioinformatics/btz870openalex-snapshot
Protein docking model evaluation by 3D deep convolutional neural networks
inferredcites →https://doi.org/10.1093/nar/gkm998openalex-snapshot
AAindex: amino acid index database, progress report 2008
inferredcites →https://doi.org/10.1093/nar/gkv368openalex-snapshot
pyDockSAXS: protein–protein complex structure by SAXS and computational docking
inferredcites →https://doi.org/10.1101/2021.09.07.459290openalex-snapshot
Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro
inferredcites →https://doi.org/10.1101/2021.10.04.463034openalex-snapshot
Protein complex prediction with AlphaFold-Multimer
inferredcites →https://doi.org/10.1107/s0907444901003122openalex-snapshot
Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI
inferredcites →https://doi.org/10.1107/s090744490201394xopenalex-snapshot
The impact of Glu→Ala and Glu→Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 Å resolution
inferredcites →https://doi.org/10.1107/s0907444903026271openalex-snapshot
The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI
inferredcites →https://doi.org/10.1107/s0907444907025784openalex-snapshot
Initial evaluations of the reproducibility of vapor-diffusion crystallization
inferredcites →https://doi.org/10.1107/s090744491003982xopenalex-snapshot
An introduction to data reduction: space-group determination, scaling and intensity statistics
inferredcites →https://doi.org/10.1107/s2053230x13033141openalex-snapshot
Introduction to protein crystallization
inferredcites →https://doi.org/10.1107/s2053230x19000141openalex-snapshot
BLAST ing away preconceptions in crystallization trials
inferredcites →https://doi.org/10.1146/annurev-biochem-013118-111947openalex-snapshot
Biophysical Techniques in Structural Biology
inferredcites →https://doi.org/10.1186/1471-2105-14-286openalex-snapshot
The scoring of poses in protein-protein docking: current capabilities and future directions
inferredcites →https://doi.org/10.1371/journal.pone.0008140openalex-snapshot
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform
inferredcites →https://doi.org/10.1371/journal.pone.0101123openalex-snapshot
Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms
inferredcites →https://doi.org/10.1371/journal.pone.0161879openalex-snapshot
DockQ: A Quality Measure for Protein-Protein Docking Models
inferredcites →https://doi.org/10.3389/fbinf.2021.693211openalex-snapshot
Quality Assessment of Protein Docking Models Based on Graph Neural Network
inferredcites →https://doi.org/10.3389/fbinf.2023.1120370openalex-snapshot
Before and after AlphaFold2: An overview of protein structure prediction
inferredcites →https://doi.org/10.3389/fmolb.2021.647915openalex-snapshot
Protein Docking Model Evaluation by Graph Neural Networks
inferredcites →https://doi.org/10.3389/fmolb.2023.1110567openalex-snapshot
Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches
inferredcites →https://doi.org/10.3390/a15110406openalex-snapshot
Stable Evaluation of 3D Zernike Moments for Surface Meshes
inferredcites →https://doi.org/10.3390/cryst11060588openalex-snapshot
Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts
inferredcites →https://doi.org/10.3390/ijms13089514openalex-snapshot
Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database
inferredcites →https://doi.org/10.3390/ijms150915122openalex-snapshot
PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions
inferredcites →https://doi.org/10.3390/molecules25051030openalex-snapshot
Protein X-ray Crystallography and Drug Discovery
inferredcites →https://doi.org/10.3934/biophy.2017.4.557openalex-snapshot
Protein crystallization: Eluding the bottleneck of X-ray crystallography

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.5281/zenodo.22926337zenodo-depositor-declared
inferred← citeshttps://doi.org/10.1093/bib/bbag233openalex-snapshot
Shoebill: an interpretable AlphaFold2-informed predictor of protein crystallization propensity using XGBoost
inferred← citeshttps://doi.org/10.5281/zenodo.22926336openalex-snapshot
Charge-sign asymmetry in protein crystallization outcomes across 52,307 purified structural-genomics targets (TargetTrack, 2017 release)
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.