Proteins-Structure Function and Bioinformatics

Article	Citations
Critical assessment of methods of protein structure prediction (CASP)—Round XIV	345
Applying and improving AlphaFold at CASP14	264
High‐accuracy protein structure prediction in CASP14	244
Human SARS CoV‐2 spike protein mutations	148
Multi‐state modeling of G‐protein coupled receptors at experimental accuracy	110
Plastics degradation by hydrolytic enzymes: Theplastics‐activeenzymes database—PAZy	103
Perturbing the energy landscape for improved packing during computational protein design	99
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	85
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges	51
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	50
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods	49
Assessing the utility of CASP14 models for molecular replacement	46
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14	40
Assessment of the CASP14 assembly predictions	40
Assessment of thePETaseconformational changes induced by poly(ethylene terephthalate) binding	39
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination	36
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes	35
New prediction categories in CASP15	35
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)	33
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	33
Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases	32
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	32
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2	32
Assessment of three‐dimensional RNA structure prediction in CASP15	32
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease	30

Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	30
Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?	30
Predicting protein flexibility with AlphaFold	30
When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14—(tFold for CASP14 contact prediction)	29
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	28
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning	28
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP	27
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic	27
Target highlights in CASP14: Analysis of models by structure providers	26
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction	25
Recent progress in the structural biology of P2X receptors	24
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐2	24
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	23
ACE2‐based decoy receptors for SARS coronavirus 2	23
Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment	22
Why are ACE2 binding coronavirus strains SARS‐CoV/SARS‐CoV‐2 wild and NL63 mild?	22
Critical assessment of methods of protein structure prediction (CASP)—Round XV	22
Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome	21
Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism	21
Improved multimer prediction using massive sampling with AlphaFold in CASP15	21
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15	21
Tertiary structure assessment at CASP15	20
Physics‐based protein structure refinement in the era of artificial intelligence	20
Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer	20
Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 2	19
Evaluation of model refinement in CASP14	19
Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations	19
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14	18
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	18
A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains	18
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability	18
Protein oligomer modeling guided by predicted interchain contacts in CASP14	17
Assessing the accuracy of contact and distance predictions in CASP14	16
RNA target highlights in CASP15: Evaluation of predicted models by structure providers	16
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15	16
Molecular dynamics simulations identify the regions of compromised thermostability in SazCA	16
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots	16
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses	15
New amino acid substitution matrix brings sequence alignments into agreement with structure matches	15
SidechainNet: An all‐atom protein structure dataset for machine learning	15
PDB‐tools web: A user‐friendly interface for the manipulation of PDB files	15
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	15
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling	15
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma	14
Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker	14
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction	14
Biological nanopores for sensing applications	14
Comparative protein structure network analysis on 3CLpro from SARS‐CoV‐1 and SARS‐CoV‐2	14
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	14
Mapping of antibody epitopes based on docking and homology modeling	14

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	14
RNA tertiary structure prediction using RNAComposer in CASP15	13
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	13
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses	13
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	13
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	12
Exploring the structure and dynamics of proteins in soil organic matter	12
Insights into the mechanisms of light‐oxygen‐voltage domain color tuning from a set of high‐resolution X‐ray structures	12
Assessment of protein–ligand complexes in CASP15	12
Protein target highlights in CASP15: Analysis of models by structure providers	11
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	11
Using normal mode analysis on protein structural models. How far can we go on our predictions?	11
RF‐SVM: Identification ofDNA‐binding proteins based on comprehensive feature representation methods and support vector machine	11
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)	10
Estimation of model accuracy in CASP15 using the ModFOLDdock server	10
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	10
Assessment of the assessment—All about complexes	10
Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation	10
RNA tertiary structure modeling with BRiQ potential in CASP15	10
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	10
Cryo‐EM targets in CASP14	10
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	10
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	10
Assessing the binding properties of CASP14 targets and models	10
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	9
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	9
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	9
Plastic structures for diverse substrates: A revisit of human ABC transporters	9
The effect of lipid composition on the dynamics of tau fibrils	9
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15	9
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	9
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	9
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors	9
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	9
Protein structure search to support the development of protein structure prediction methods	9
From propensities to patterns to principles in protein folding	8
Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target	8
Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis	8
Ca2+ as cofactor of the mitochondrial H+‐translocating F1FO‐ATP(hydrol)ase	8
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	8
Automated benchmarking of combined protein structure and ligand conformation prediction	8
Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes	8
Calcium inhibits penetration of Alzheimer's Aβ1–42 monomers into the membrane	8
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	8
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	8
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15	8
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics study	8
Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites	8
Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding	8
Inferring metal binding sites in flexible regions of proteins	8
β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils	7
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15	7
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks	7
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	7
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	7
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	7
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	7
Do “Newly Born” orphan proteins resemble “Never Born” proteins? A study using three deep learning algorithms	7
Isolation and characterization of ACE‐I inhibitory peptides from ribbonfish for a potential inhibitor of the main protease of SARS‐CoV‐2: An in silico analysis	7
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	7
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	7
Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis	7
A geometrical framework for thinking about proteins	7
ANOVA‐particle swarm optimization‐based feature selection and gradient boosting machine classifier for improved protein–protein interaction prediction	7
Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor	7
A detailed mapping of the readily accessible disulphide bonds in the cortex of wool fibres	7
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues	7
Structures and interactions of insulin‐like peptides from cone snail venom	6
Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins	6
Crystal‐structures‐guided design of fragment‐based drugs for inhibiting the main protease of SARS‐CoV‐2	6
Introduction of a new scheme for classifying β‐turns in protein structures	6
Predicting mutant outcome by combining deep mutational scanning and machine learning	6
Circuit topology predicts pathogenicity of missense mutations	6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	6
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	6
Scoring of protein–protein docking models utilizing predicted interface residues	6
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium	6
Insights into modular polyketide synthase loops aided by repetitive sequences	6
Random, de novo, and conserved proteins: How structure and disorder predictors perform differently	6
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	6

Ca2+ ions facilitate the organization of the Annexin A2/S100A10 heterotetramer	6
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	6
Proteome analysis of the circadian clock protein PERIOD2	6
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study	6
Conformation of myelin basic protein bound to phosphatidylinositol membrane characterized by vacuum‐ultraviolet circular‐dichroism spectroscopy and molecular‐dynamics simulations	6
The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils	6
Novel antimicrobial anionic cecropins from the spruce budworm feature a poly‐L‐aspartic acid C‐terminus	6
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors	6
The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors	6
Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase	6
A computer aided drug discovery based discovery of lead‐like compounds against KDM5A for cancers using pharmacophore modeling and high‐throughput virtual screening	6
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints	6
Are granulins copper sequestering proteins?	6
Total free energy analysis of fully hydrated proteins	5
Exploring CCRL2 chemerin binding using accelerated molecular dynamics	5
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF2	5
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	5
Inhibition of Mycobacterium tuberculosisInhA by 3‐nitropropanoic acid	5
Characterization of glutamate‐cysteine ligase and glutathione synthetase from the δ‐proteobacterium Myxococcus xanthus	5
The X‐ray crystal structure of human A15C neuroglobin reveals both native/de novo disulfide bonds and unexpected ligand‐binding sites	5
Structural and functional analysis of the human cone‐rod homeobox transcription factor	5
The role of leucine and isoleucine in tuning the hydropathy of class A GPCRs	5
Study on functional sites in human multidrug resistance protein 1 (hMRP1)	5
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	5
The protonation state of Glu202 in acetylcholinesterase	5
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	5
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane	5
Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B	5
New tyrosinases with putative action against contaminants of emerging concern	5
Benchmarking of structure refinement methods for protein complex models	5
Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol‐phosphate dehydratase	5
Simplified geometric representations of protein structures identify complementary interaction interfaces	5
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	5
Ligands‐induced open‐close conformational change during DapE catalysis: Insights from molecular dynamics simulations	5
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase	5
Protein oligomer structure prediction using GALAXY in CASP14	5
Identification of key molecular players and associated pathways in cervical squamous cell carcinoma progression through network analysis	5
Sequence and evolutionary analysis of bacterial ribosomal S1 proteins	5
Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites	5
Protein dynamics analysis identifies candidate cancer driver genes and mutations inTCGAdata	5
Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide	5
Pep–Whisperer: Inhibitory peptide design	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	5
The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing	5
zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15	4
Antibody mutations favoring pH‐dependent binding in solid tumor microenvironments: Insights from large‐scale structure‐based calculations	4
Mutual information analysis of mutation, nonlinearity, and triple interactions in proteins	4
Structural basis for binding of the renal carcinoma target hypoxia‐inducible factor 2α to prolyl hydroxylase domain 2	4
The dynamic basis of structural order in proteins	4
A novel consensus‐based computational pipeline for screening of antibody therapeutics for efficacy against SARS‐CoV‐2 variants of concern including Omicron variant	4
Counter‐intuitive enhancement of degradation of polyethylene terephthalate through engineering of lowered enzyme binding to solid plastic	4
Analysis of CheW‐like domains provides insights into organization of prokaryotic chemotaxis systems	4
Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β‐catenin and TRIB pseudokinases	4
DeepCys: Structure‐based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains	4
Protein structure prediction using the evolutionary algorithm USPEX	4
Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single‐particle cryo‐EM	4
Influence of ALS‐linked M337V mutation on the conformational ensembles of TDP‐43321–340 peptide monomer and dimer	4
Remarked suppression of Aβ42 protomer–protomer dissociation reaction elucidated by molecular dynamics simulation	4
Insight into the structural basis of the dual inhibitory mode of Lima bean (Phaseolus lunatus) serine protease inhibitor	4
A monomeric structure of human TMEM63A protein	4
II. Geometrical framework for thinking about globular proteins: The power of poking	4
In silico screening and molecular dynamics simulation of deleterious PAH mutations responsible for phenylketonuria genetic disorder	4
Dockground scoring benchmarks for protein docking	4
Dynamics in an unusual acyl carrier protein from a ladderane lipid‐synthesizing organism	4
Multi‐layer sequential network analysis improves protein3Dstructural classification	4
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	4
Comprehensive folding variations for protein folding	4
Effects of ion type and concentration on the structure and aggregation of the amyloid peptide Aβ16−22$$ {\boldsymbol{\beta}}_{16-22} $$	4
Molecular dynamics simulations reveal the disruption mechanism of a 2,4‐thiazolidinedione derivative C30 against tau hexapeptide (PHF6) oligomer	4
A Maximum Caliber analysis of the Foldon Hypothesis	4
Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis	4
Identification, analysis, and modeling of the YUCCA protein family genome‐wide in Coffea canephora	4
Annexin A1, A2, A5, and A6 involvement in human pathologies	4
Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Prediction of protein–protein interactions using sequences of intrinsically disordered regions	4
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	4
Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins	4
Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies	4
Structural and biochemical studies of an iterative ribosomal peptide macrocyclase	4
Substrate‐assisted activation and selectivity of the bacterial RavD effector deubiquitinylase	4
Biophysical characterization of full‐length oleosin in dodecylphosphocholine micelles	4
Evidence for the preferential reuse of sub‐domain motifs in primordial protein folds	4
Interplay between hydrogen and chalcogen bonds in cysteine	4
Structural insights at acidic pH of dye‐decolorizing peroxidase from Bacillus subtilis	4
The ChaC1 active site: Defining the residues and determining the role of ChaC1‐exclusive residues in the structural and functional stability	3
Dimerization underlies the aggregation propensity of intrinsically disordered coiled‐coil domain‐containing 124	3
IGF‐dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2	3
Structural modeling of peptide toxin–ion channel interactions using RosettaDock	3
The energetics and evolution of oxidoreductases in deep time	3
Unraveling the role of flexible coil near calcium binding site of levansucrase on thermostability and product profile via proline substitution and molecular dynamics simulations	3
A study of a hierarchical structure of proteins and ligand binding sites of receptors using the triangular spatial relationship‐based structure comparison method and development of a size‐filtering fe	3