On the public citation graph
xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.
0 signed · 165 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.
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known work and none has been retracted — and get a dated CiteStamped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.
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(20000801)40:2<237::aid-prot60>3.0.co;2-popenalex-snapshot
Toward an energy function for the contact map representation of proteins
inferredcites →https://doi.org/10.1002/bip.360221211openalex-snapshot
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
inferredcites →https://doi.org/10.1002/jcc.21688openalex-snapshot
Wordom: A user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
inferredcites →https://doi.org/10.1002/pro.558openalex-snapshot
Exploring the factors determining the dynamics of different protein folds
inferredcites →https://doi.org/10.1002/pro.710openalex-snapshot
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
inferredcites →https://doi.org/10.1002/prot.20232openalex-snapshot
Is allostery an intrinsic property of all dynamic proteins?
inferredcites →https://doi.org/10.1002/prot.20784openalex-snapshot
Generalized correlation for biomolecular dynamics
inferredcites →https://doi.org/10.1002/prot.22553openalex-snapshot
A perturbative view of protein structural variation
inferredcites →https://doi.org/10.1002/prot.22711openalex-snapshot
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
inferredcites →https://doi.org/10.1002/prot.22995openalex-snapshot
Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches
inferredcites →https://doi.org/10.1006/jmbi.1995.0514openalex-snapshot
Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1007/s00018-009-0014-6openalex-snapshot
Functional aspects of protein flexibility
inferredcites →https://doi.org/10.1007/s00018-010-0519-zopenalex-snapshot
Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor
inferredcites →https://doi.org/10.1007/s00239-009-9225-6openalex-snapshot
What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor?
inferredcites →https://doi.org/10.1007/s00723-012-0314-0openalex-snapshot
MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL
inferredcites →https://doi.org/10.1007/s10822-010-9352-6openalex-snapshot
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
inferredcites →https://doi.org/10.1007/s10822-010-9395-8openalex-snapshot
Computer-aided drug design platform using PyMOL
inferredcites →https://doi.org/10.1007/s10822-011-9465-6openalex-snapshot
VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
inferredcites →https://doi.org/10.1016/j.bbamem.2010.08.006openalex-snapshot
Dimerization and ligand binding affect the structure network of A2A adenosine receptor
inferredcites →https://doi.org/10.1016/j.bbapap.2008.05.011openalex-snapshot
The conserved N-terminal helix of acylpeptide hydrolase from archaeon Aeropyrum pernix K1 is important for its hyperthermophilic activity
inferredcites →https://doi.org/10.1016/j.bbapap.2009.10.017openalex-snapshot
Defining the conserved internal architecture of a protein kinase
inferredcites →https://doi.org/10.1016/j.bpc.2011.05.020openalex-snapshot
The role of protein conformational fluctuations in allostery, function, and evolution
inferredcites →https://doi.org/10.1016/j.bpj.2010.08.079openalex-snapshot
Interaction Energy Based Protein Structure Networks
inferredcites →https://doi.org/10.1016/j.febslet.2007.05.021openalex-snapshot
Network analysis of protein dynamics
inferredcites →https://doi.org/10.1016/j.febslet.2008.02.048openalex-snapshot
Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin‐like serine‐proteases
inferredcites →https://doi.org/10.1016/j.gene.2008.06.002openalex-snapshot
Evolutionary conservation of protein vibrational dynamics
inferredcites →https://doi.org/10.1016/j.jmb.2003.07.014openalex-snapshot
Temperature Adaptation of Proteins: Engineering Mesophilic-like Activity and Stability in a Cold-adapted α-Amylase
inferredcites →https://doi.org/10.1016/j.jmb.2008.02.034openalex-snapshot
Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play
inferredcites →https://doi.org/10.1016/j.jmb.2012.01.052openalex-snapshot
Multistate Allostery in Response Regulators: Phosphorylation and Mutagenesis Activate RegA via Alternate Modes
inferredcites →https://doi.org/10.1016/j.jmgm.2011.07.008openalex-snapshot
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
inferredcites →https://doi.org/10.1016/j.jsb.2008.09.003openalex-snapshot
Coevolving residues of (β/α)8-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics
inferredcites →https://doi.org/10.1016/j.jsb.2011.01.006openalex-snapshot
Dynamic properties of extremophilic subtilisin-like serine-proteases
inferredcites →https://doi.org/10.1016/j.jsb.2012.04.003openalex-snapshot
C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes
inferredcites →https://doi.org/10.1016/j.sbi.2006.01.003openalex-snapshot
The changing landscape of protein allostery
inferredcites →https://doi.org/10.1016/j.sbi.2009.03.004openalex-snapshot
Long-timescale molecular dynamics simulations of protein structure and function
inferredcites →https://doi.org/10.1016/j.str.2009.12.015openalex-snapshot
Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily
inferredcites →https://doi.org/10.1016/j.tibs.2007.03.008openalex-snapshot
eMovie: a storyboard-based tool for making molecular movies
inferredcites →https://doi.org/10.1016/j.tibs.2010.04.009openalex-snapshot
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
inferredcites →https://doi.org/10.1016/j.tibs.2011.01.002openalex-snapshot
Analyzing and visualizing residue networks of protein structures
inferredcites →https://doi.org/10.1021/ja202587aopenalex-snapshot
Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties
inferredcites →https://doi.org/10.1021/ja210751topenalex-snapshot
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation
inferredcites →https://doi.org/10.1021/ja809915aopenalex-snapshot
Conservation of Side-Chain Dynamics Within a Protein Family
inferredcites →https://doi.org/10.1021/ja907476wopenalex-snapshot
Toward a Unified Representation of Protein Structural Dynamics in Solution
inferredcites →https://doi.org/10.1021/pr0602388openalex-snapshot
Protein Intrinsic Disorder and Human Papillomaviruses: Increased Amount of Disorder in E6 and E7 Oncoproteins from High Risk HPVs
inferredcites →https://doi.org/10.1038/nature03199openalex-snapshot
Simultaneous determination of protein structure and dynamics
inferredcites →https://doi.org/10.1038/nprot.2012.004openalex-snapshot
Topological analysis and interactive visualization of biological networks and protein structures
inferredcites →https://doi.org/10.1038/sj.embor.7401160openalex-snapshot
Molecular simulations of protein dynamics: new windows on mechanisms in biology
inferredcites →https://doi.org/10.1039/c2cp41224aopenalex-snapshot
Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation
inferredcites →https://doi.org/10.1073/pnas.0408930102openalex-snapshot
Molecular dynamics and protein function
inferredcites →https://doi.org/10.1073/pnas.0409128102openalex-snapshot
Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis
inferredcites →https://doi.org/10.1073/pnas.0510426103openalex-snapshot
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
inferredcites →https://doi.org/10.1073/pnas.0605534104openalex-snapshot
A consensus view of protein dynamics
inferredcites →https://doi.org/10.1073/pnas.0704459104openalex-snapshot
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
inferredcites →https://doi.org/10.1089/106652704773416876openalex-snapshot
1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap
inferredcites →https://doi.org/10.1093/bioinformatics/btp304openalex-snapshot
FlexServ: an integrated tool for the analysis of protein flexibility
inferredcites →https://doi.org/10.1093/bioinformatics/btq566openalex-snapshot
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes
inferredcites →https://doi.org/10.1093/bioinformatics/btr163openalex-snapshot
CMView: Interactive contact map visualization and analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btr168openalex-snapshot
ProDy : Protein Dynamics Inferred from Theory and Experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btr191openalex-snapshot
RING: networking interacting residues, evolutionary information and energetics in protein structures
inferredcites →https://doi.org/10.1093/nar/gki404openalex-snapshot
MutDB services: interactive structural analysis of mutation data
inferredcites →https://doi.org/10.1093/nar/gkn769openalex-snapshot
Voronoia: analyzing packing in protein structures
inferredcites →https://doi.org/10.1093/nar/gkq360openalex-snapshot
CCRXP: exploring clusters of conserved residues in protein structures
inferredcites →https://doi.org/10.1110/ps.03259908openalex-snapshot
Allostery and cooperativity revisited
inferredcites →https://doi.org/10.1186/1471-2105-13-s4-s2openalex-snapshot
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
inferredcites →https://doi.org/10.1186/1471-2105-7-316openalex-snapshot
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
inferredcites →https://doi.org/10.1371/journal.pcbi.0030172openalex-snapshot
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
inferredcites →https://doi.org/10.1371/journal.pcbi.0040043openalex-snapshot
Accurate Structural Correlations from Maximum Likelihood Superpositions
inferredcites →https://doi.org/10.1371/journal.pcbi.1000323openalex-snapshot
Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer
inferredcites →https://doi.org/10.1371/journal.pcbi.1000574openalex-snapshot
Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1000738openalex-snapshot
On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm
inferredcites →https://doi.org/10.1371/journal.pcbi.1002023openalex-snapshot
“Fluctuograms” Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
inferredcites →https://doi.org/10.1371/journal.pcbi.1002428openalex-snapshot
Collective Dynamics Differentiates Functional Divergence in Protein Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0017459openalex-snapshot
The Contribution of Coevolving Residues to the Stability of KDO8P Synthase
inferredcites →https://doi.org/10.1371/journal.pone.0020665openalex-snapshot
The Loss of the p53 Activator HIPK2 Is Responsible for Galectin-3 Overexpression in Well Differentiated Thyroid Carcinomas
inferredcites →https://doi.org/10.1371/journal.pone.0024214openalex-snapshot
Molecular Dynamics of Mesophilic-Like Mutants of a Cold-Adapted Enzyme: Insights into Distal Effects Induced by the Mutations
inferredcites →https://doi.org/10.1371/journal.pone.0032131openalex-snapshot
Systematic Validation of Protein Force Fields against Experimental Data
inferredcites →https://doi.org/10.1371/journal.pone.0035686openalex-snapshot
Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation
inferredcites →https://doi.org/10.1529/biophysj.104.053041openalex-snapshot
Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family
inferredcites →https://doi.org/10.1529/biophysj.105.064485openalex-snapshot
A Network Representation of Protein Structures: Implications for Protein Stability
inferredcites →https://doi.org/10.1529/biophysj.105.074997openalex-snapshot
Investigating the Local Flexibility of Functional Residues in Hemoproteins
inferredcites →https://doi.org/10.1529/biophysj.107.105270openalex-snapshot
Allosteric Transitions in the Chaperonin GroEL are Captured by a Dominant Normal Mode that is Most Robust to Sequence Variations
inferredcites →https://doi.org/10.2174/138920309787847590openalex-snapshot
Intra and Inter-Molecular Communications Through Protein Structure Network
inferredcites →https://doi.org/10.2174/1875036201105010053openalex-snapshot
GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures
inferredcites →https://doi.org/10.4161/cc.10.1.14345openalex-snapshot
Chemical states of the N-terminal “lid” of MDM2 regulate p53 binding: Simulations reveal complexities of modulation
inferredcites →https://doi.org/10.6026/97320630002346openalex-snapshot
PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4826459openalex-extracted
Spectrochemical, Antimicrobial and Pharmacological Studies of Some Arylidene-Malononitrile and Ethyl-2-Cyano-3-Phenylacrylate Derivatives
inferred← citeshttps://doi.org/10.1002/9783527806836.ch6openalex-snapshot
Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science
inferred← citeshttps://doi.org/10.1002/pro.2333openalex-snapshot
An automated approach to network features of protein structure ensembles
inferred← citeshttps://doi.org/10.1002/prot.24460openalex-snapshot
Molecular dynamics study of HIV‐1 RT‐DNA‐nevirapine complexes explains NNRTI inhibition and resistance by connection mutations
inferred← citeshttps://doi.org/10.1007/978-1-0716-1154-8_10openalex-snapshot
The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles
inferred← citeshttps://doi.org/10.1007/978-1-0716-1154-8_13openalex-snapshot
Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations
inferred← citeshttps://doi.org/10.1007/978-1-4939-9608-7_18openalex-snapshot
Analyzing Biomolecular Ensembles
inferred← citeshttps://doi.org/10.1007/978-3-030-05282-9_3openalex-snapshot
Analysis of Protein Structures Using Residue Interaction Networks
inferred← citeshttps://doi.org/10.1007/s00726-014-1710-6openalex-snapshot
The construction of an amino acid network for understanding protein structure and function
inferred← citeshttps://doi.org/10.1007/s00726-015-1927-zopenalex-snapshot
Manganese superoxide dismutase from human pathogen Clostridium difficile
inferred← citeshttps://doi.org/10.1007/s00894-014-2450-yopenalex-snapshot
Analysis of the structure and dynamics of human serum albumin
inferred← citeshttps://doi.org/10.1007/s00894-020-04508-zopenalex-snapshot
PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids
inferred← citeshttps://doi.org/10.1016/j.amolm.2026.100105openalex-snapshot
Synthesis, characterization, antimicrobial evaluation, pharmacokinetic and QSAR studies of some novel acrylates: in vitro and in silico approach
inferred← citeshttps://doi.org/10.1016/j.bbagen.2012.12.011openalex-snapshot
Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase
inferred← citeshttps://doi.org/10.1016/j.bbagen.2013.07.007openalex-snapshot
The conformational ensemble of the disordered and aggregation-protective 182–291 region of ataxin-3
inferred← citeshttps://doi.org/10.1016/j.bbagen.2017.05.018openalex-snapshot
Dissecting intrinsic and ligand-induced structural communication in the β3 headpiece of integrins
inferred← citeshttps://doi.org/10.1016/j.bbagen.2020.129605openalex-snapshot
Conformational gating in ammonia lyases
inferred← citeshttps://doi.org/10.1016/j.bbamem.2016.01.010openalex-snapshot
Computational approaches to detect allosteric pathways in transmembrane molecular machines
inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.09.018openalex-snapshot
Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2023.108094openalex-snapshot
Role of distal sites in enzyme engineering
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2025.108788openalex-snapshot
From traditional to AI-driven: The evolution of intelligent enzyme engineering for biocatalysis
inferred← citeshttps://doi.org/10.1016/j.chroma.2018.02.016openalex-snapshot
Automating data analysis for two-dimensional gas chromatography/time-of-flight mass spectrometry non‐targeted analysis of comparative samples
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104929openalex-snapshot
Structural probing of HapR to identify potent phytochemicals to control Vibrio cholera through integrated computational approaches
inferred← citeshttps://doi.org/10.1016/j.csbj.2016.06.002openalex-snapshot
Biophysical and computational methods to analyze amino acid interaction networks in proteins
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.12.044openalex-snapshot
PSNtools for standalone and web-based structure network analyses of conformational ensembles
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2026.151855openalex-snapshot
Cooperative engineering of distal and proximal domains in L-alanine dehydrogenase breaks activity-stability trade-off for efficient hydroxypyruvic acid synthesis
inferred← citeshttps://doi.org/10.1016/j.jmb.2021.167123openalex-snapshot
Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A?
inferred← citeshttps://doi.org/10.1016/j.jpba.2023.115540openalex-snapshot
Unveiling differential mechanisms of chuanxiong cortex and pith in the treatment of coronary heart disease using SPME-GC×GC-MS and network pharmacology
inferred← citeshttps://doi.org/10.1016/j.lfs.2023.122321openalex-snapshot
Fenofibrate inhibits MOXD1 and PDZK1IP1 expression and improves lipid deposition and inflammation in mice with alcoholic fatty liver
inferred← citeshttps://doi.org/10.1016/j.pharmthera.2013.01.016openalex-snapshot
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
inferred← citeshttps://doi.org/10.1016/j.psj.2024.104571openalex-snapshot
HSP60 inhibits DF-1 apoptosis through its mitochondrial signal peptide
inferred← citeshttps://doi.org/10.1016/j.str.2015.02.013openalex-snapshot
CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00742openalex-snapshot
Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins bycorrelationplus
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00973openalex-snapshot
Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00512openalex-snapshot
(Dis)similarity Index To Compare Correlated Motions in Molecular Simulations
inferred← citeshttps://doi.org/10.1021/ci400639ropenalex-snapshot
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins
inferred← citeshttps://doi.org/10.1038/s41467-018-05722-3openalex-snapshot
HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα
inferred← citeshttps://doi.org/10.1038/s41598-017-01498-6openalex-snapshot
An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
inferred← citeshttps://doi.org/10.1039/9781788010139-00198openalex-snapshot
Uncovering GPCR and G Protein Function by Protein Structure Network Analysis
inferred← citeshttps://doi.org/10.1039/c4fd00024bopenalex-snapshot
Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs
inferred← citeshttps://doi.org/10.1039/c6ra06312hopenalex-snapshot
The dynamics of the β-propeller domain in Kelch protein KLHL40 changes upon nemaline myopathy-associated mutation
inferred← citeshttps://doi.org/10.1042/bcj20200799openalex-snapshot
Weakening of interaction networks with aging in tip-link protein induces hearing loss
inferred← citeshttps://doi.org/10.1080/07391102.2019.1588169openalex-snapshot
Spectral analysis of molecular dynamics simulations on PDZ: MD sectors
inferred← citeshttps://doi.org/10.1080/07391102.2023.2199083openalex-snapshot
Fascin − F-actin interaction studied by molecular dynamics simulation and protein network analysis
inferred← citeshttps://doi.org/10.1080/07391102.2023.2201360openalex-snapshot
Elucidation of bezlotoxumab binding specificity to toxin B in Clostridioides difficile
inferred← citeshttps://doi.org/10.1080/15548627.2020.1847443openalex-snapshot
The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer
inferred← citeshttps://doi.org/10.1080/23746149.2022.2080587openalex-snapshot
Computational methods and theory for ion channel research
inferred← citeshttps://doi.org/10.1093/bib/bbac074openalex-snapshot
MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles
inferred← citeshttps://doi.org/10.1093/bib/bbz029openalex-snapshot
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
inferred← citeshttps://doi.org/10.1093/nar/gkaa397openalex-snapshot
webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules
inferred← citeshttps://doi.org/10.1093/nar/gkw383openalex-snapshot
NAPS: Network Analysis of Protein Structures
inferred← citeshttps://doi.org/10.1093/nar/gkw770openalex-snapshot
DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions
inferred← citeshttps://doi.org/10.1093/nar/gky381openalex-snapshot
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
inferred← citeshttps://doi.org/10.1093/nar/gkz390openalex-snapshot
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
inferred← citeshttps://doi.org/10.1093/nar/gkz399openalex-snapshot
NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes
inferred← citeshttps://doi.org/10.1101/2025.08.04.653638openalex-snapshot
Interpreting the Effects of DNA Polymerase Variants at the Structural Level Using MAVISp and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1126/sciadv.abg3815openalex-snapshot
Activation mechanism of Drosophila cryptochrome through an allosteric switch
inferred← citeshttps://doi.org/10.11606/d.76.2013.tde-09042013-114356openalex-snapshot
Estudos estruturais da proteína PelD de Pseudomonas aeruginosa: um receptor de c-di-GMP responsável pela produção de exopolissacarídeos e formação de biofilmes
inferred← citeshttps://doi.org/10.1177/10241221261446763openalex-snapshot
Antibacterial evaluation, quantum chemical computation, and pharmacological studies of some arylidenemalononitrile and ethyl 2-cyano-3-phenylacrylate derivatives: In vitro and in silico approach
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003744openalex-snapshot
Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005826openalex-snapshot
Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
inferred← citeshttps://doi.org/10.1371/journal.pone.0255167openalex-snapshot
pyProGA—A PyMOL plugin for protein residue network analysis
inferred← citeshttps://doi.org/10.1371/journal.pone.0265194openalex-snapshot
SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations
inferred← citeshttps://doi.org/10.2174/1389203711314020004openalex-snapshot
The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory
inferred← citeshttps://doi.org/10.2174/1389557516999160612163350openalex-snapshot
Protein Structure Network-based Drug Design
inferred← citeshttps://doi.org/10.3389/fcvm.2022.804801openalex-snapshot
Exploring the Mechanism of Hawthorn Leaves Against Coronary Heart Disease Using Network Pharmacology and Molecular Docking
inferred← citeshttps://doi.org/10.3389/fmolb.2015.00028openalex-snapshot
Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity
inferred← citeshttps://doi.org/10.3389/fmolb.2021.658312openalex-snapshot
Conformational Characterization of the Co-Activator Binding Site Revealed the Mechanism to Achieve the Bioactive State of FXR
inferred← citeshttps://doi.org/10.3389/fphys.2012.00435openalex-snapshot
Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation
inferred← citeshttps://doi.org/10.3390/molecules27196475openalex-snapshot
Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug–Protein Binding
inferred← citeshttps://doi.org/10.7287/peerj.11552v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11552v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11552v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.5998v0.1/reviews/1openalex-snapshot
Peer Review #1 of "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5998v0.1/reviews/2openalex-snapshot
Peer Review #2 of "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5998v0.1/reviews/3openalex-snapshot
Peer Review #3 of "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.5998v0.2/reviews/2openalex-snapshot
Peer Review #2 of "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.5998v0.2/reviews/3openalex-snapshot
Peer Review #3 of "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.11552openalex-snapshot
Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
inferred← citeshttps://doi.org/10.7717/peerj.5998openalex-snapshot
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
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.