Performance of ZDOCK in CAPRI rounds 20–26

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2013-12-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1002/prot.24432PMID 24123140PMCID PMC3975700
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Binding interface prediction by combining protein–protein docking results

  2014cited by this paper
• Blind prediction of interfacial water positions in CAPRI

  2014cited by this paper
• Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

  2013cited by this paper
• Exploring Angular Distance in Protein-Protein Docking Algorithms

  2013cited by this paper
• Ranking multiple docking solutions based on the conservation of inter‐residue contacts

  2013cited by this paper
• Prediction of protein–protein binding free energies

  2012cited by this paper
• Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

  2011cited by this paper
• Integrating atom‐based and residue‐based scoring functions for protein–protein docking

  2011cited by this paper
• ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

  2011cited by this paper
• CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

  2011cited by this paper
• A structure‐based benchmark for protein–protein binding affinity

  2011cited by this paper
• Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

  2011cited by this paper
• Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein

  2011cited by this paper
• Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

  2011cited by this paper
• The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

  2010cited by this paper
• Building Macromolecular Assemblies by Information-driven Docking

  2010cited by this paper
• Performance of ZDOCK and ZRANK in CAPRI rounds 13–19

  2010cited by this paper
• Structure of a fibronectin type III-like module from Clostridium thermocellum.

  2010cited by this paper
• Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats.

  2010cited by this paper
• Structure‐based design of a T‐cell receptor leads to nearly 100‐fold improvement in binding affinity for pepMHC

  2009cited by this paper
• CHARMM: The biomolecular simulation program

  2009cited by this paper
• Protein structure prediction on the Web: a case study using the Phyre server

  2009cited by this paper
• Antibody Recognition of a Highly Conserved Influenza Virus Epitope

  2009influential reference
• Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions

  2008influential reference
• A combination of rescoring and refinement significantly improves protein docking performance

  2008cited by this paper
• Structural consequences of effector protein complex formation in a diiron hydroxylase

  2008cited by this paper
• Protein–protein docking benchmark version 3.0

  2008cited by this paper
• Structure and mode of action of a mosquitocidal holotoxin.

  2008cited by this paper
• Integrating statistical pair potentials into protein complex prediction

  2007cited by this paper
• Redox and functional analysis of the Rieske ferredoxin component of the toluene 4-monooxygenase.

  2007cited by this paper
• A holistic approach to protein docking

  2007cited by this paper
• ZRANK: Reranking protein docking predictions with an optimized energy function

  2007cited by this paper
• The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI

  2007cited by this paper
• Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.

  2006cited by this paper
• Structures of in vitro evolved binding sites on neocarzinostatin scaffold reveal unanticipated evolutionary pathways.

  2006cited by this paper
• ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

  2005cited by this paper
• Prediction of multimolecular assemblies by multiple docking.

  2005cited by this paper
• Data‐driven docking: HADDOCK's adventures in CAPRI

  2005cited by this paper
• Identification of protein-protein interaction sites from docking energy landscapes.

  2004cited by this paper
• Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

  2003cited by this paper
• CAPRI: A Critical Assessment of PRedicted Interactions

  2003cited by this paper
• ZDOCK: An initial‐stage protein‐docking algorithm

  2003cited by this paper
• ZDOCK predictions for the CAPRI challenge

  2003cited by this paper
• A novel shape complementarity scoring function for protein‐protein docking

  2003cited by this paper
• A simple physical model for binding energy hot spots in protein–protein complexes

  2002influential reference
• High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.

  2002cited by this paper
• Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM

  2001cited by this paper
• Prediction of protein interaction sites from sequence profile and residue neighbor list

  2001cited by this paper
• Comparative protein modelling by satisfaction of spatial restraints.

  1993cited by this paper

• AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.

  2025cites this paper
• Properties of human centrin 2 and cooperative effects between the N- and C-terminal domains

  2025cites this paper
• PKIB facilitates bladder cancer proliferation and metastasis through mediation of HSP27 phosphorylation by PKA

  2025cites this paper
• A TRIM Family-Based Strategy for TRIMCIV Target Prediction in a Pan-Cancer Context with Multi-Omics Data and Protein Docking Integration

  2025cites this paper
• A TRPV1 agonist from the transcriptome profiling of Dipsastraea rotumana inhibits neuroinflammation in vivo through the NF-κB and MAPK pathways.

  2025cites this paper
• Molecular Basis for the Involvement of Mammalian Serum Albumin in the AGE/RAGE Axis: A Comprehensive Computational Study

  2024cites this paper
• Targeted drug delivery to the thrombus by fusing streptokinase with a fibrin-binding peptide (CREKA): an in silico study.

  2024cites this paper
• Interaction of Glycated Albumin with Receptor for Glycation End Products According to Molecular Modeling Data

  2023cites this paper
• Anti-epileptic Kunitz-like peptides discovered in the branching coral Acropora digitifera through transcriptomic analysis

  2022cites this paper
• Phosphorylation promotes the endonuclease-like activity of human centrin 2

  2022cites this paper
• Performance of ZDOCK and IRAD in CAPRI rounds 39‐45

  2020cites this paper
• GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations

  2019cites this paper
• Modelling and Computational Sequence Analysis of a Bacteriocin Isolated from Bacillus licheniformis strain BTHT8

  2018cites this paper
• Integrating cross-linking experiments with ab initio protein-protein docking

  2018cites this paper
• Interactions of the major histocompatibility complex class I BF2*15 and cytotoxic T lymphocyte epitopes from nucleoprotein of avian infectious bronchitis virus

  2017cites this paper
• Performance of ZDOCK and IRAD in CAPRI rounds 28–34

  2017cites this paper
• Prediction of Biomolecular Complexes

  2017cites this paper
• AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

  2017cites this paper
• Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

  2017cites this paper
• Computational modeling of protein assemblies.

  2017cites this paper
• Molecular Docking at a Glance

  2016cites this paper
• Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

  2016cites this paper
• Estimating binding free energy of a putative growth factors EGF–VEGF complex – a computational bioanalytical study

  2016cites this paper
• Exploration of the BF2*15 major histocompatibility complex class I binding motif and identification of cytotoxic T lymphocyte epitopes from the H5N1 influenza virus nucleoprotein in chickens

  2016cites this paper
• Computational analysis of the CB1 carboxyl‐terminus in the receptor‐G protein complex

  2016cites this paper
• Studying the binding interactions of allosteric agonists and antagonists of the CXCR4 receptor.

  2015cites this paper
• Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

  2015cites this paper
• ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

  2014cites this paper
• Integrative computational modeling of protein interactions

  2014cites this paper
• Search strategies and evaluation in protein-protein docking: principles, advances and challenges.

  2014cites this paper