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Development and testing of an automated approach to protein docking
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Estimating relative free energies from a single ensemble: Hydration free energies
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Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
inferredcites →https://doi.org/10.1002/(sici)1097-0282(199609)39:3<455::aid-bip16>3.0.co;2-aopenalex-snapshot
Low-resolution docking: Prediction of complexes for underdetermined structures
inferredcites →https://doi.org/10.1002/1097-0134(20010501)43:2<89::aid-prot1021>3.0.co;2-hopenalex-snapshot
Residue frequencies and pairing preferences at protein-protein interfaces
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.340200405openalex-snapshot
Hydrophobic docking: A proposed enhancement to molecular recognition techniques
inferredcites →https://doi.org/10.1007/0-387-24532-4_6openalex-snapshot
Protein-Protein Docking Methods
inferredcites →https://doi.org/10.1016/j.jmb.2004.09.051openalex-snapshot
Protein–Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking
inferredcites →https://doi.org/10.1016/j.tibtech.2004.01.006openalex-snapshot
Protein–protein docking: is the glass half-full or half-empty?
inferredcites →https://doi.org/10.1073/pnas.0401942101openalex-snapshot
Anchor residues in protein–protein interactions
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/10.1073/pnas.96.15.8477openalex-snapshot
A systematic study of low-resolution recognition in protein–protein complexes
inferredcites →https://doi.org/10.1093/bioinformatics/19.1.163openalex-snapshot
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
inferredcites →https://doi.org/10.1093/protein/8.4.371openalex-snapshot
Protein docking for low-resolution structures
inferredcites →https://doi.org/10.1093/protein/9.1.37openalex-snapshot
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction
inferredcites →https://doi.org/10.1110/ps.0304503openalex-snapshot
The role of geometric complementarity in secondary structure packing: A systematic docking study
inferredcites →https://doi.org/10.1110/ps.8701openalex-snapshot
How common is the funnel‐like energy landscape in protein‐protein interactions?
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Protein Structure and Function Prediction Using I‐TASSER
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Protein–protein docking dealing with the unknown
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Using correlated parameters for improved ranking of protein–protein docking decoys
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SDOCK: A global protein‐protein docking program using stepwise force‐field potentials
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Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions
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A protein‐specifically adapted scoring function for the reranking of docking solutions
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Identification of near‐native structures by clustering protein docking conformations
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A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
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Large‐scale characteristics of the energy landscape in protein–protein interactions
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The size of the intermolecular energy funnel in protein–protein interactions
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Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes
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Detection and refinement of encounter complexes for protein–protein docking: Taking account of macromolecular crowding
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Improving ranking of models for protein complexes with side chain modeling and atomic potentials
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DockRank: Ranking docked conformations using partner‐specific sequence homology‐based protein interface prediction
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Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization
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A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC
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Rescore protein-protein docked ensembles with an interface contact statistics
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Fine tuning rigid body docking results using the Dreiding force field: A computational study of 36 known nanobody‐protein complexes
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Comparative Modeling of Proteins
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Protein–Protein Docking: Overview and Performance Analysis
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Immunoinformatics-driven design of a conserved RNA-dependent RNA polymerase-based multi-epitope vaccine against avian infectious bronchitis virus
inferred← citeshttps://doi.org/10.14288/1.0307160openalex-snapshot
Identifying and characterizing caveolin-1 derived peptides : a novel approach to promoting nitric oxide release from the endothelium
inferred← citeshttps://doi.org/10.1529/biophysj.108.132977openalex-snapshot
Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions
inferred← citeshttps://doi.org/10.17537/2011.6.53openalex-snapshot
On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers
inferred← citeshttps://doi.org/10.17537/2011.6.92openalex-snapshot
Molecular dynamic of the complexes of (RADA)4 - the self-organizing ionic peptides
inferred← citeshttps://doi.org/10.17537/2012.7.493openalex-snapshot
RISM integral equation theory in study of thermodynamics of self-assembling ionic peptides
inferred← citeshttps://doi.org/10.17537/2018.13.t29openalex-snapshot
On The Choice of Force Fields for Studying the Molecular Dynamics of Ion Peptides and Their Dimers
inferred← citeshttps://doi.org/10.17760/d20439215openalex-snapshot
Elucidating replication dynamics involving the alpha subunit of DNA polymerase III and single stranded DNA binding protein in E. coli
inferred← citeshttps://doi.org/10.20948/prepr-2019-72openalex-snapshot
Biogels. On comparison of structure differences in anti-parallel and parallel complexes with syn-layers of the H-(RADA)4-OH peptides.
inferred← citeshttps://doi.org/10.21203/rs.2.13688/v1openalex-snapshot
In silico prediction of structural and functional effects of the E71G mutation on GARS and its role in CMT2D and HMN5A pathogenesis
inferred← citeshttps://doi.org/10.2174/138161213804581882openalex-snapshot
ADP-Ribosylated Proteins as Old and New Drug Targets for Anticancer Therapy: The Example of ARF6
inferred← citeshttps://doi.org/10.2174/138920308783565741openalex-snapshot
Recent Progress and Future Directions in Protein-Protein Docking
inferred← citeshttps://doi.org/10.2174/1874199100903010075openalex-snapshot
Molecular Docking Simulation of Short-Chain Four Disulphide Bridged Scorpion Toxins with Structural Model of Human Voltage-Gated Potassium Ion Channel Kv1.3
inferred← citeshttps://doi.org/10.2174/1874199100903020075openalex-snapshot
Molecular Docking Simulation of Short-Chain Four Disulphide Bridged Scorpion Toxins with Structural Model of Human Voltage-Gated Potassium Ion Channel Kv1.
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.643openalex-snapshot
Use of Protein Crosslinking and Tandem Mass Spectrometry to Study the PsbO, PsbP and PsbQ Extrinsic Proteins of Higher Plant Photosystem II
inferred← citeshttps://doi.org/10.31857/s0132342323030107openalex-snapshot
Dynamics of 24 Self-Assembling H-(RADA)4-OH Peptides Complexed in Bi-Layered Structure with Layers in syn and anti Orientation
inferred← citeshttps://doi.org/10.3389/falgy.2022.877553openalex-snapshot
Gibberellin-regulated proteins: Emergent allergens
inferred← citeshttps://doi.org/10.3389/fmolb.2021.647915openalex-snapshot
Protein Docking Model Evaluation by Graph Neural Networks
inferred← citeshttps://doi.org/10.3390/biom11070934openalex-snapshot
Cloning and Characterization of Aedes aegypti Trypsin Modulating Oostatic Factor (TMOF) Gut Receptor
inferred← citeshttps://doi.org/10.3390/biom14050574openalex-snapshot
A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models
inferred← citeshttps://doi.org/10.3390/cancers13205130openalex-snapshot
Enhanced IFNα Signaling Promotes Ligand-Independent Activation of ERα to Promote Aromatase Inhibitor Resistance in Breast Cancer
inferred← citeshttps://doi.org/10.3390/ijms11103623openalex-snapshot
SwarmDock and the Use of Normal Modes in Protein-Protein Docking
inferred← citeshttps://doi.org/10.3390/ijms22169081openalex-snapshot
Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
inferred← citeshttps://doi.org/10.3390/life13010019openalex-snapshot
Bactericidal Properties of Proline-Rich Aedes aegypti Trypsin Modulating Oostatic Factor (AeaTMOF)
inferred← citeshttps://doi.org/10.3390/molecules200611569openalex-snapshot
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
inferred← citeshttps://doi.org/10.3390/molecules23113018openalex-snapshot
Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.3390/physics5040073openalex-snapshot
Theory of Liquids for Studying the Conformational Flexibility of Biomolecules with Reference Interaction Site Model Approximation
inferred← citeshttps://doi.org/10.3390/v15122297openalex-snapshot
Computational Analysis of CD46 Protein Interaction with SARS-CoV-2 Structural Proteins: Elucidating a Putative Viral Entry Mechanism into Human Cells
inferred← citeshttps://doi.org/10.3390/vaccines10101660openalex-snapshot
Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2
inferred← citeshttps://doi.org/10.3390/zoonoticdis2030012openalex-snapshot
Host–Virus Interactions in Japanese Encephalitis Virus
inferred← citeshttps://doi.org/10.37868/hsd.v2i1.32openalex-snapshot
Interactome analysis and docking sites prediction of (AtCHR8, AtCUL4 and AtERCC1/UVR7) proteins in Arabidopsis Thaliana
inferred← citeshttps://doi.org/10.3866/pku.whxb201209172openalex-snapshot
Protein-Protein Interaction: Prediction, Design, and Modulation
inferred← citeshttps://doi.org/10.3892/ijmm.2018.3395openalex-snapshot
Dengue virus-1 NS5 genetic variant associated with a severe clinical infection: Possible reduction of the innate immune response by inhibition of interferon type 1 and the Janus kinase-signal transducer and activator of transcription signaling pathway
inferred← citeshttps://doi.org/10.4155/fmc.13.204openalex-snapshot
Structure-Based Design of Small-Molecule Protein–Protein Interaction Modulators: The Story so Far
inferred← citeshttps://doi.org/10.4172/2161-0517.1000115openalex-snapshot
Molecular Modeling and Interaction Studies of HCV Core Protein
inferred← citeshttps://doi.org/10.4172/2329-6798.1000108openalex-snapshot
Tumor Differentiation Factor (TDF) and its Receptor (TDF-R): Is TDF-R an Inducible Complex with Multiple Docking Sites?
inferred← citeshttps://doi.org/10.4172/2329-6798.1000126openalex-snapshot
Structural Investigation of HSP70-HSP90 and HSP90-TDF Interactions
inferred← citeshttps://doi.org/10.5772/intechopen.74733openalex-snapshot
Cellular Interaction of Human Eukaryotic Elongation Factor 1A Isoforms
inferred← citeshttps://doi.org/10.5821/dissertation-2117-109356openalex-snapshot
Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest
inferred← citeshttps://doi.org/10.70675/9f63a212z2148z4952za179z025cba3f7eb1openalex-snapshot
Pairwise and Multi-Component Protein-Protein Docking Using Exhaustive Branch-and-Bound Tri-Dimensional Rotational Searches
inferred← citeshttps://doi.org/10.70675/bfdded7czb638z455azaedaz4ae9f8d0a13dopenalex-snapshot
New computational approaches to study the effect of genetic mutations on the topology of protein-protein interaction networks
inferred← citeshttps://doi.org/10.7774/cevr.2024.13.3.202openalex-snapshot
Insights into structural vaccinology harnessed for universal coronavirus vaccine development
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