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Selection of near‐native poses in CAPRI rounds 13‐19

https://doi.org/10.1002/prot.22772
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What this work says

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

inferredcites →https://doi.org/10.1002/pro.5560060902openalex-snapshot
Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of alzheimer's amyloid β‐protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): Engineering of inhibitors with altered specificities
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ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10460openalex-snapshot
RDOCK: Refinement of rigid‐body protein docking predictions
inferredcites →https://doi.org/10.1002/prot.1099openalex-snapshot
Prediction of protein interaction sites from sequence profile and residue neighbor list
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Sequence–structure–function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site‐directed mutagenesis
inferredcites →https://doi.org/10.1002/prot.20514openalex-snapshot
Prediction of interface residues in protein–protein complexes by a consensus neural network method: Test against NMR data
inferredcites →https://doi.org/10.1002/prot.20563openalex-snapshot
Data‐driven docking: HADDOCK's adventures in CAPRI
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.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21752openalex-snapshot
A holistic approach to protein docking
inferredcites →https://doi.org/10.1002/prot.21759openalex-snapshot
Automatic prediction of protein interactions with large scale motion
inferredcites →https://doi.org/10.1002/prot.22726openalex-snapshot
Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer
inferredcites →https://doi.org/10.1016/0022-2836(91)80221-fopenalex-snapshot
Refined crystal structure of the complex of subtilisin BPN′ and Streptomyces subtilisin inhibitor at 1·8Åresolution
inferredcites →https://doi.org/10.1016/j.jmb.2004.02.040openalex-snapshot
ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites
inferredcites →https://doi.org/10.1016/j.jmb.2007.05.015openalex-snapshot
A Genome-wide Ras-Effector Interaction Network
inferredcites →https://doi.org/10.1016/j.jmb.2007.06.068openalex-snapshot
Recognition Elements in rRNA for the Tylosin Resistance Methyltransferase RlmAII
inferredcites →https://doi.org/10.1016/j.jmb.2008.05.034openalex-snapshot
Structural and Mutational Analyses of the Interaction between the Barley α-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition
inferredcites →https://doi.org/10.1016/j.jmgm.2003.12.005openalex-snapshot
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
inferredcites →https://doi.org/10.1016/j.str.2007.10.025openalex-snapshot
Structure of the Yeast tRNA m7G Methylation Complex
inferredcites →https://doi.org/10.1016/s0006-291x(03)01187-2openalex-snapshot
Centaurin-α1 associates with and is phosphorylated by isoforms of protein kinase C
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/s0969-2126(03)00076-5openalex-snapshot
Design of Stable α-Helical Arrays from an Idealized TPR Motif
inferredcites →https://doi.org/10.1016/s0969-2126(98)00066-5openalex-snapshot
Barley α-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 å resolution
inferredcites →https://doi.org/10.1016/s1097-2765(00)00114-3openalex-snapshot
The Molecular Basis of FHA Domain:Phosphopeptide Binding Specificity and Implications for Phospho-Dependent Signaling Mechanisms
inferredcites →https://doi.org/10.1017/s1355838202024019openalex-snapshot
Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA
inferredcites →https://doi.org/10.1021/bi9808621openalex-snapshot
Dual Recognition and the Role of Specificity-Determining Residues in Colicin E9 DNase−Immunity Protein Interactions
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1038/emboj.2009.209openalex-snapshot
The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4
inferredcites →https://doi.org/10.1038/nsb920openalex-snapshot
Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
inferredcites →https://doi.org/10.1038/nsmb714openalex-snapshot
Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1
inferredcites →https://doi.org/10.1073/pnas.0400189101openalex-snapshot
Crystal structure of RlmA I : Implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site
inferredcites →https://doi.org/10.1073/pnas.0910756107openalex-snapshot
The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction
inferredcites →https://doi.org/10.1074/jbc.272.35.22253openalex-snapshot
Protein-Protein Interaction Specificity of Im9 for the Endonuclease Toxin Colicin E9 Defined by Homologue-scanning Mutagenesis
inferredcites →https://doi.org/10.1074/jbc.m109.022095openalex-snapshot
The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation
inferredcites →https://doi.org/10.1074/jbc.m303047200openalex-snapshot
Direct Interaction of Rnd1 with Plexin-B1 Regulates PDZ-RhoGEF-mediated Rho Activation by Plexin-B1 and Induces Cell Contraction in COS-7 Cells
inferredcites →https://doi.org/10.1074/jbc.m311947200openalex-snapshot
Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases.
inferredcites →https://doi.org/10.1074/jbc.m412222200openalex-snapshot
Mutational Analysis of Target Enzyme Recognition of the β-Trefoil Fold Barley α-Amylase/Subtilisin Inhibitor
inferredcites →https://doi.org/10.1074/jbc.m703800200openalex-snapshot
Binding of Rac1, Rnd1, and RhoD to a Novel Rho GTPase Interaction Motif Destabilizes Dimerization of the Plexin-B1 Effector Domain
inferredcites →https://doi.org/10.1093/bioinformatics/bti229openalex-snapshot
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
inferredcites →https://doi.org/10.1093/bioinformatics/bti322openalex-snapshot
FastContact: rapid estimate of contact and binding free energies
inferredcites →https://doi.org/10.1093/bioinformatics/btm434openalex-snapshot
meta-PPISP: a meta web server for protein-protein interaction site prediction
inferredcites →https://doi.org/10.1093/nar/gkl454openalex-snapshot
Protein binding site prediction using an empirical scoring function
inferredcites →https://doi.org/10.1107/s0108767309097438openalex-snapshot
Putting an N-terminal end to theClostridium thermocellumxylanase Xyn10B story: structure of the CBM22-1-GH10 modules complexed with xylohexaose
inferredcites →https://doi.org/10.1111/j.1432-1033.1994.00507.xopenalex-snapshot
Crystallographic Studies of Savinase, a Subtilisin‐like Proteinase, at pH 10.5
inferredcites →https://doi.org/10.1242/jcs.02369openalex-snapshot
Centaurin-α1 interacts directly with kinesin motor protein KIF13B
inferredcites →https://doi.org/10.1261/rna.2030705openalex-snapshot
tRNA m7G methyltransferase Trm8p/Trm82p: Evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p
inferredcites →https://doi.org/10.1371/journal.pcbi.1000191openalex-snapshot
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118889886.ch4openalex-snapshot
Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment
inferred← citeshttps://doi.org/10.1002/prot.22850openalex-snapshot
Blind predictions of protein interfaces by docking calculations in CAPRI
inferred← citeshttps://doi.org/10.1002/prot.23179openalex-snapshot
On the use of distance constraints in protein–protein docking computations
inferred← citeshttps://doi.org/10.1002/prot.24366openalex-snapshot
Using the concept of transient complex for affinity predictions in CAPRI rounds 20–27 and beyond
inferred← citeshttps://doi.org/10.1002/prot.25234openalex-snapshot
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
inferred← citeshttps://doi.org/10.1007/978-1-0716-3985-6_12openalex-snapshot
Challenges of Protein-Protein Docking of the Membrane Proteins
inferred← citeshttps://doi.org/10.1007/s12551-012-0086-7openalex-snapshot
PI2PE: a suite of web servers for predictions ranging from protein structure to binding kinetics
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/10.1088/1478-3975/8/3/035006openalex-snapshot
Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces
inferred← citeshttps://doi.org/10.2174/138920311796957694openalex-snapshot
Structural Models of Protein-DNA Complexes Based on Interface Prediction and Docking
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