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Performance of ZDOCK and ZRANK in CAPRI rounds 13–19

https://doi.org/10.1002/prot.22764
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What this work says

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

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CHARMM: The biomolecular simulation program
inferredcites →https://doi.org/10.1002/prot.10334openalex-snapshot
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.10388openalex-snapshot
ZDOCK predictions for the CAPRI challenge
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.20454openalex-snapshot
Sequence–structure–function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site‐directed mutagenesis
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.20559openalex-snapshot
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
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.21502openalex-snapshot
Integrating statistical pair potentials into protein complex prediction
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The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
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Protein–protein docking benchmark version 3.0
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Basic Local Alignment Search Tool
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Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes
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Recognition Elements in rRNA for the Tylosin Resistance Methyltransferase RlmAII
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Structural and Mutational Analyses of the Interaction between the Barley α-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition
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Prediction of MEF2A–DNA interface by rigid body docking: A tool for fast estimation of protein mutational effects on DNA binding
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Structure of the Yeast tRNA m7G Methylation Complex
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Protein Structure Prediction Using Rosetta
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Barley α-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 å resolution
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The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein
inferredcites →https://doi.org/10.1021/bi0106742openalex-snapshot
Clostridium thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding,
inferredcites →https://doi.org/10.1021/bi962993copenalex-snapshot
Two Reactive Site Locations and Structure−Function Study of the Arrowhead Proteinase Inhibitors, A and B, Using Mutagenesis
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/bi992821qopenalex-snapshot
The X6 “Thermostabilizing” Domains of Xylanases Are Carbohydrate-Binding Modules: Structure and Biochemistry of the Clostridium thermocellum X6b Domain,
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/10.1042/bj2930151openalex-snapshot
Arginine is essential for the α-amylase inhibitory activity of the α-amylase/subtilisin inhibitor (BASI) from barley seeds
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.112332899openalex-snapshot
A clogged gutter mechanism for protease inhibitors
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.m311911200openalex-snapshot
Structural Insights into the Interaction of ROCKI with the Switch Regions of RhoA
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/10.1107/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/10.1126/science.1097545openalex-snapshot
The Semaphorin 4D Receptor Plexin-B1 Is a GTPase Activating Protein for R-Ras
inferredcites →https://doi.org/10.1242/jcs.02369openalex-snapshot
Centaurin-α1 interacts directly with kinesin motor protein KIF13B

What points at this work

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

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