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H‐bond network optimization in protein–protein complexes: Are all‐atom force field scores enough?

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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/(sici)1097-0134(199710)29:2<172::aid-prot5>3.0.co;2-fopenalex-snapshot

Understanding the recognition of protein structural classes by amino acid composition

inferredcites →https://doi.org/10.1002/jcc.21409openalex-snapshot

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

inferredcites →https://doi.org/10.1002/prot.10393openalex-snapshot

Assessment of blind predictions of protein–protein interactions: Current status of docking methods

inferredcites →https://doi.org/10.1002/prot.10613openalex-snapshot

A hierarchical approach to all‐atom protein loop prediction

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.20560openalex-snapshot

Protein–protein docking benchmark 2.0: An update

inferredcites →https://doi.org/10.1002/prot.21125openalex-snapshot

Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling

inferredcites →https://doi.org/10.1002/prot.21419openalex-snapshot

pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking

inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot

Integrating statistical pair potentials into protein complex prediction

inferredcites →https://doi.org/10.1002/prot.21579openalex-snapshot

Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking

inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot

Docking and scoring protein complexes: CAPRI 3rd Edition

inferredcites →https://doi.org/10.1002/prot.22564openalex-snapshot

Present and future challenges and limitations in protein–protein docking

inferredcites →https://doi.org/10.1002/prot.22830openalex-snapshot

Protein–protein docking benchmark version 4.0

inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot

Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton

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.jmb.2007.07.050openalex-snapshot

Protein–Protein Docking with Backbone Flexibility

inferredcites →https://doi.org/10.1016/s0022-2836(02)00470-9openalex-snapshot

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

inferredcites →https://doi.org/10.1021/ct0501811openalex-snapshot

PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique

inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

inferredcites →https://doi.org/10.1021/jm800071vopenalex-snapshot

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

inferredcites →https://doi.org/10.1021/jp037821lopenalex-snapshot

First-Shell Solvation of Ion Pairs: Correction of Systematic Errors in Implicit Solvent Models

inferredcites →https://doi.org/10.1093/protein/14.1.1openalex-snapshot

Conformational change of proteins arising from normal mode calculations

inferredcites →https://doi.org/10.1110/ps.0239303openalex-snapshot

Protein–protein docking with a reduced protein model accounting for side‐chain flexibility

inferredcites →https://doi.org/10.2174/157340908784533265openalex-snapshot

How to Efficiently Include Receptor Flexibility During Computational Docking

What points at this work

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

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Improving ranking of models for protein complexes with side chain modeling and atomic potentials

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How binding to surfaces affects disorder?

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A theoretical multiscale treatment of protein–protein electron transfer: The ferredoxin/ferredoxin-NADP+ reductase and flavodoxin/ferredoxin-NADP+ reductase systems

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PURA and GLUT1: Sweet partners for brain health

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2013.05.004openalex-snapshot

H-bond refinement for electron transfer membrane-bound protein–protein complexes: Cytochrome c oxidase and cytochrome c552

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2013.12.003openalex-snapshot

Collective variable driven molecular dynamics to improve protein–protein docking scoring

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Study on the interaction of artificial and natural food colorants with human serum albumin: A computational point of view

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Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia

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Structural Hotspot Conditioning for Diffusion-Based Molecular Design

inferred← citeshttps://doi.org/10.1021/bi500814topenalex-snapshot

Flexible Docking-Based Molecular Dynamics/Steered Molecular Dynamics Calculations of Protein–Protein Contacts in a Complex of Cytochrome P450 1A2 with Cytochrome b 5

inferred← citeshttps://doi.org/10.1039/c3cp50484kopenalex-snapshot

Electron transfer in proteins: theory, applications and future perspectives

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Tryptogalinin Is a Tick Kunitz Serine Protease Inhibitor with a Unique Intrinsic Disorder

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Enhanced sampling for lipid-protein interactions during membrane dynamics

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Mapping biophysics through enhanced Monte Carlo techniques

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