Shape complementarity of protein–protein complexes at multiple resolutions

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2009-05-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1002/prot.22256PMID 18837463PMCID PMC2928789
• 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.

• Minimal molecular surfaces and their applications

  2008cited by this paper
• Determination of the interfacial water content in protein-protein complexes from free energy simulations.

  2006cited by this paper
• What role do surfaces play in GB models? A new‐generation of surface‐generalized born model based on a novel gaussian surface for biomolecules

  2006cited by this paper
• Revisiting the description of Protein-Protein interfaces. Part II: Experimental study

  2006cited by this paper
• Protein–protein docking benchmark 2.0: An update

  2005influential reference
• The effect of resolution‐dependent global shape modifications on rigid‐body protein–protein docking

  2005cited by this paper
• Compressed representations of macromolecular structures and properties.

  2005cited by this paper
• A novel shape complementarity scoring function for protein‐protein docking

  2003influential reference
• The tissue factor/factor VIIa/factor Xa complex: A model built by docking and site‐directed mutagenesis

  2003cited by this paper
• Role of water mediated interactions in protein-protein recognition landscapes.

  2003cited by this paper
• Gaussian docking functions.

  2003cited by this paper
• Assessment of blind predictions of protein–protein interactions: Current status of docking methods

  2003cited by this paper
• Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking.

  2003cited by this paper
• Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2

  2003cited by this paper
• Evaluation of Protein Docking Predictions Using Hex 3.1 in CAPRI Rounds 1{2

  2002cited by this paper
• Docking unbound proteins using shape complementarity, desolvation, and electrostatics

  2002influential reference
• Protein docking using a genetic algorithm

  2001cited by this paper
• Protein docking using spherical polar Fourier correlations

  2000cited by this paper
• Optimization of Gaussian surface calculations and extension to solvent‐accessible surface areas

  1999cited by this paper
• A systematic study of low-resolution recognition in protein--protein complexes.

  1999cited by this paper
• Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces

  1999cited by this paper
• Examination of shape complementarity in docking of Unbound proteins

  1999cited by this paper
• Low-resolution docking: prediction of complexes for underdetermined structures.

  1998cited by this paper
• Accelerated IsoContouring of Scalar Fields

  1998cited by this paper
• Modelling protein docking using shape complementarity, electrostatics and biochemical information.

  1997cited by this paper
• Prediction of protein conformational freedom from distance constraints

  1997cited by this paper
• Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking.

  1996cited by this paper
• Analytically defined surfaces to analyze molecular interaction properties.

  1996cited by this paper
• Fast isocontouring for improved interactivity

  1996cited by this paper
• A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

  1996cited by this paper
• A Gaussian Description of Molecular Shape

  1995cited by this paper
• Fast and robust computation of molecular surfaces

  1995cited by this paper
• A geometry-based suite of molecular docking processes.

  1995cited by this paper
• Protein docking for low-resolution structures.

  1995cited by this paper
• A quantitative representation of molecular surface shape. I: Theory and development of the method

  1994cited by this paper
• Shape complementarity at protein–protein interfaces

  1994cited by this paper
• PUZZLE: a new method for automated protein docking based on surface shape complementarity.

  1994cited by this paper
• Approximation and characterization of molecular surfaces

  1993cited by this paper
• Shape analysis of molecular surfaces

  1993cited by this paper
• Shape complementarity at protein/protein interfaces.

  1993cited by this paper
• On gray scale image measurements : II. Surface area and volume

  1991influential reference
• "Soft docking": matching of molecular surface cubes.

  1991cited by this paper
• Solid shape

  1990cited by this paper
• Description of molecular surface shape using Fourier descriptors

  1988cited by this paper
• Spherical harmonic molecular surfaces

  1988cited by this paper
• Analytical molecular surface calculation

  1983cited by this paper
• A Generalization of Algebraic Surface Drawing

  1982cited by this paper

• Helix α1 of human ACE2 mimics dsDNA and Spike of SARS-CoV-2 binds DNA.

  2025cites this paper
• SHREC2024: Non-rigid Complementary Shapes Retrieval in Protein-protein Interactions

  2024cites this paper
• The Nature of Intermolecular Interactions Affecting Oligomerization of Nt.BspD6I Nickase

  2024cites this paper
• Exploiting Copaifera salikounda compounds as treatment against diabetes: An insight into their potential targets from a computational perspective

  2023cites this paper
• Computational designing of the ligands of Protein L affinity chromatography based on molecular docking and molecular dynamics simulations

  2023cites this paper
• Antimicrobial Activity and Molecular Docking of Benzoyl-N,N’-dialkylurea against Target Proteins in Microbial Cells

  2023cites this paper
• EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations

  2023cites this paper
• A bioinformatic approach of targeting SARS-CoV-2 replication by silencing a conserved alternative reserve of the orf8 gene using host miRNAs

  2022cites this paper
• Size of the protein-protein energy funnel in crowded environment

  2022cites this paper
• Resources for Docking-Based Virtual Screening

  2021cites this paper
• 2D Zernike polynomial expansion: Finding the protein-protein binding regions

  2020cites this paper
• Complementarity in Complex Networks

  2020cites this paper
• Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 ofMycobacterium tuberculosis

  2019cites this paper
• Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance

  2019cites this paper
• Strukturne in termodinamske osnove interakcij globularnih in intrinzično neurejenih proteinov

  2019cites this paper
• Classification and Scoring of Protein Complexes

  2019cites this paper
• Structural Basis of Epitope Recognition by Heavy-Chain Camelid Antibodies.

  2018cites this paper
• Engineered protein scaffolds as leads for synthetic inhibitors of protein-protein interactions.

  2018cites this paper
• Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance

  2018cites this paper
• The design of target specific antibodies (scFv) by applying de novo workflow: Case study on BmR1 antigen from Brugia malayi.

  2017cites this paper
• An in silico approach to understand the structure–function properties of a serine protease (Bacifrinase) from Bacillus cereus and experimental evidence to support the interaction of Bacifrinase with fibrinogen and thrombin

  2017cites this paper
• Rotation of artificial rotor axles in rotary molecular motors

  2016cites this paper
• Shaping the Information Channel: Molecules, Cells, and Experiments

  2016cites this paper
• Predicting Protein-Protein Binding Affinity by In silico Docking

  2016cites this paper
• Geometric and statistical methods for the analysis and prediction of structural interactions between biomolecules. (Méthodes géométriques et statistiques pour l'analyse et la prédiction des interactions structurales de biomolécules)

  2015cites this paper
• Protein-protein docking: from interaction to interactome.

  2014cites this paper
• Molecular modeling of protein–protein interaction to decipher the structural mechanism of nonhost resistance in rice

  2014cites this paper
• Protein–protein alternative binding modes do not overlap

  2013cites this paper
• Structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain involved in the targeting of tail-anchored membrane proteins to the endoplasmic reticulum.

  2013cites this paper
• Low-resolution structural modeling of protein interactome.

  2013cites this paper
• Comparative Modeling of Serotonin Receptors 5ht2a and 5ht2c and In-silico Investigationof their Potential as Off-Target to Ethinylestradiol

  2013cites this paper
• Protein-protein interactions and prediction: a comprehensive overview.

  2013cites this paper
• Multiscale modeling of macromolecular

  2012cites this paper
• Multiscale modeling of macromolecular biosystems

  2012cites this paper
• Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints

  2012cites this paper
• Protein-protein interfaces integrated into interaction networks: implications on drug design.

  2012cites this paper
• Protein-protein binding affinities calculated using the LIE method

  2011cites this paper
• Multiscale Protein and Peptide Docking

  2011cites this paper
• Flexible Protein-Protein Docking

  2011cites this paper
• PROTEIN SURFACE SIMILARITIES EVALUATION FOR FUNCTIONAL ANNOTATION STUDIES

  2010cites this paper
• Accounting for conformational changes during protein-protein docking.

  2010cites this paper
• Protein-protein docking using region-based 3D Zernike descriptors

  2009cites this paper