On the public citation graph

Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets

https://doi.org/10.1002/prot.20565

0 signed · 66 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/1097-0134(20000815)40:3<389::aid-prot50>3.0.co;2-2openalex-snapshot

The penultimate rotamer library

inferredcites →https://doi.org/10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-fopenalex-snapshot

Scoring docked conformations generated by rigid-body protein-protein docking

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot

CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot

CAPRI: A Critical Assessment of PRedicted Interactions

inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot

ZDOCK: An initial‐stage protein‐docking algorithm

inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot

Successful discrimination of protein interactions

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.20564openalex-snapshot

Performance of the first protein docking server ClusPro in CAPRI rounds 3–5

inferredcites →https://doi.org/10.1006/jmbi.1996.0859openalex-snapshot

Determination of atomic desolvation energies from the structures of crystallized proteins

inferredcites →https://doi.org/10.1007/s008940100045openalex-snapshot

GROMACS 3.0: a package for molecular simulation and trajectory analysis

inferredcites →https://doi.org/10.1016/0022-2836(71)90324-xopenalex-snapshot

The interpretation of protein structures: Estimation of static accessibility

inferredcites →https://doi.org/10.1016/s0006-3495(01)76044-4openalex-snapshot

Dynamical View of the Positions of Key Side Chains in Protein-Protein Recognition

inferredcites →https://doi.org/10.1021/bi011853mopenalex-snapshot

Duplicated Dockerin Subdomains of Clostridium thermocellum Endoglucanase CelD Bind to a Cohesin Domain of the Scaffolding Protein CipA with Distinct Thermodynamic Parameters and a Negative Cooperativity

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/nature01873openalex-snapshot

Complex between nidogen and laminin fragments reveals a paradigmatic β-propeller interface

inferredcites →https://doi.org/10.1038/nature02582openalex-snapshot

Structural basis of protein phosphatase 1 regulation

inferredcites →https://doi.org/10.1073/pnas.0400014101openalex-snapshot

Insight into the PrP C → PrP Sc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants

inferredcites →https://doi.org/10.1073/pnas.0401942101openalex-snapshot

Anchor residues in protein–protein interactions

inferredcites →https://doi.org/10.1073/pnas.181147798openalex-snapshot

Protein docking along smooth association pathways

inferredcites →https://doi.org/10.1073/pnas.1936124100openalex-snapshot

Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex

inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

inferredcites →https://doi.org/10.1074/jbc.m404212200openalex-snapshot

Structural Basis for Inhibition of Aspergillus niger Xylanase by Triticum aestivum Xylanase Inhibitor-I

inferredcites →https://doi.org/10.1093/bioinformatics/btg211openalex-snapshot

Consensus alignment for reliable framework prediction in homology modeling

inferredcites →https://doi.org/10.1093/bioinformatics/btg371openalex-snapshot

ClusPro: an automated docking and discrimination method for the prediction of protein complexes

inferredcites →https://doi.org/10.1093/bioinformatics/bti322openalex-snapshot

FastContact: rapid estimate of contact and binding free energies

inferredcites →https://doi.org/10.1093/emboj/16.8.1876openalex-snapshot

Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1

inferredcites →https://doi.org/10.1145/224170.224218openalex-snapshot

Surveying molecular interactions with DOT

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118183373.ch9openalex-snapshot

Binding Promiscuity of Unfolded Peptides

inferred← citeshttps://doi.org/10.1002/9781118523063.ch8openalex-snapshot

Virtual Ligand Screening Against Comparative Models of Proteins

inferred← citeshttps://doi.org/10.1002/jcc.21170openalex-snapshot

Computational chemistry study of 3D‐structure‐function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials

inferred← citeshttps://doi.org/10.1002/prot.20932openalex-snapshot

Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions

inferred← citeshttps://doi.org/10.1002/prot.21906openalex-snapshot

Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach

inferred← citeshttps://doi.org/10.1002/prot.22488openalex-snapshot

Improved prediction of protein side‐chain conformations with SCWRL4

inferred← citeshttps://doi.org/10.1002/prot.22564openalex-snapshot

Present and future challenges and limitations in protein–protein docking

inferred← citeshttps://doi.org/10.1002/wcms.45openalex-snapshot

Prediction of protein binding sites and hot spots

inferred← citeshttps://doi.org/10.1007/978-1-4614-4723-8_2openalex-snapshot

Background

inferred← citeshttps://doi.org/10.1007/978-1-4614-4723-8_5openalex-snapshot

Conclusion

inferred← citeshttps://doi.org/10.1007/978-3-319-09976-7_7openalex-snapshot

Molecular Mechanics/Coarse-Grained Models

inferred← citeshttps://doi.org/10.1007/978-3-642-24855-9_25openalex-snapshot

Using Kendall-τ Meta-Bagging to Improve Protein-Protein Docking Predictions

inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00250-9openalex-snapshot

Structural, Energetic, and Dynamic Aspects of Ligand–Receptor Interactions

inferred← citeshttps://doi.org/10.1016/b978-8-1312-2297-3.50007-2openalex-snapshot

Protein Interactions

inferred← citeshttps://doi.org/10.1016/j.bbrc.2018.01.160openalex-snapshot

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations

inferred← citeshttps://doi.org/10.1016/j.bpc.2006.09.014openalex-snapshot

The structure at 2 Å resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC–PC complex

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2007.03.010openalex-snapshot

Simulation of conformational changes occurring when a protein interacts with its receptor

inferred← citeshttps://doi.org/10.1016/j.csbj.2019.12.007openalex-snapshot

Computational reconstruction of atomistic protein structures from coarse-grained models

inferred← citeshttps://doi.org/10.1016/j.jmb.2009.12.053openalex-snapshot

Rapid Structural Characterization of Human Antibody–Antigen Complexes through Experimentally Validated Computational Docking

inferred← citeshttps://doi.org/10.1016/j.jsamd.2017.03.001openalex-snapshot

Multi-scale simulations of membrane proteins: The case of bitter taste receptors

inferred← citeshttps://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot

Flexible protein–protein docking

inferred← citeshttps://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot

High-resolution protein–protein docking

inferred← citeshttps://doi.org/10.1021/ci9003706openalex-snapshot

Molecular Docking Screens Using Comparative Models of Proteins

inferred← citeshttps://doi.org/10.1021/ct600236qopenalex-snapshot

Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale: Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding Link Module of TSG-6

inferred← citeshttps://doi.org/10.1021/pr060651fopenalex-snapshot

Modeling Protein−Protein Complexes Involved in the Cytochrome c Oxidase Copper-Delivery Pathway

inferred← citeshttps://doi.org/10.1039/c8cp03826kopenalex-snapshot

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

inferred← citeshttps://doi.org/10.1093/bib/bbp001openalex-snapshot

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti322openalex-snapshot

FastContact: rapid estimate of contact and binding free energies

inferred← citeshttps://doi.org/10.1093/nar/gkl206openalex-snapshot

GRAMM-X public web server for protein-protein docking

inferred← citeshttps://doi.org/10.1093/nar/gkm326openalex-snapshot

FastContact: a free energy scoring tool for protein-protein complex structures

inferred← citeshttps://doi.org/10.1093/nar/gkp1132openalex-snapshot

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains

inferred← citeshttps://doi.org/10.1093/nar/gkq502openalex-snapshot

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000490openalex-snapshot

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

inferred← citeshttps://doi.org/10.1371/journal.pone.0089466openalex-snapshot

DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking

inferred← citeshttps://doi.org/10.1517/17460440903002067openalex-snapshot

Docking and scoring: applications to drug discovery in the interactomics era

inferred← citeshttps://doi.org/10.2147/aabc.s6272openalex-snapshot

Computer applications for prediction of protein–protein interactions and rational drug design

inferred← citeshttps://doi.org/10.2174/138920308783565741openalex-snapshot

Recent Progress and Future Directions in Protein-Protein Docking

inferred← citeshttps://doi.org/10.3390/ijms12021410openalex-snapshot

Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

inferred← citeshttps://doi.org/10.5772/20865openalex-snapshot

Flexible Protein-Protein Docking

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.