Proteins-Structure Function and Bioinformatics

Article	Citations
Critical assessment of methods of protein structure prediction (CASP)—Round XIV	279
Applying and improving AlphaFold at CASP14	224
High‐accuracy protein structure prediction in CASP14	210
Human SARS CoV‐2 spike protein mutations	142
Perturbing the energy landscape for improved packing during computational protein design	80
Multi‐state modeling of G‐protein coupled receptors at experimental accuracy	80
Plastics degradation by hydrolytic enzymes: The plastics‐active enzymes database—PAZy	79
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment	69
Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges	47
Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14	46
Assessing the utility of CASP14 models for molecular replacement	41
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods	40
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14	37
Assessment of the CASP14 assembly predictions	36
Computational models in the service of X‐ray and cryo‐electron microscopy structure determination	35
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)	32
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)	32
Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes	31
Assessment of thePETaseconformational changes induced by poly(ethylene terephthalate) binding	31
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2	29
When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14—(tFold for CASP14 contact prediction)	27
Repurposing of FDA‐approved drugs against active site and potential allosteric drug‐binding sites of COVID‐19 main protease	27
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP	27
Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain	27
Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor	27

Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases	26
Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?	26
Evolutionary relationships and sequence‐structure determinants in human SARS coronavirus‐2 spike proteins for host receptor recognition	25
Target highlights in CASP14: Analysis of models by structure providers	25
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning	24
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures	24
Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic	23
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction	22
Multicopper oxidases: modular structure, sequence space, and evolutionary relationships	22
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?	21
ACE2‐based decoy receptors for SARS coronavirus 2	20
Using machine learning to improve ensemble docking for drug discovery	19
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS‐CoV‐2	19
Evaluation of model refinement in CASP14	19
DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins	19
Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations	18
Recent progress in the structural biology of P2X receptors	18
Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer	18
New prediction categories in CASP15	18
Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14	18
Predicting protein flexibility with AlphaFold	18
Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome	17
Physics‐based protein structure refinement in the era of artificial intelligence	17
Integrated bioinformatics–cheminformatics approach toward locating pseudo‐potential antiviral marine alkaloids against SARS‐CoV‐2‐Mpro	17
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability	17
Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism	16
Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism	16
Protein oligomer modeling guided by predicted interchain contacts in CASP14	15
Molecular dynamics simulations identify the regions of compromised thermostability in SazCA	15
Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting	15
Assessing the accuracy of contact and distance predictions in CASP14	15
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15	15
New amino acid substitution matrix brings sequence alignments into agreement with structure matches	14
SidechainNet: An all‐atom protein structure dataset for machine learning	14
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14	14
An in silico scientific basis for LL‐37 as a therapeutic for Covid‐19	14
The actin cytoskeleton orchestra in Entamoeba histolytica	13
Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies	13
A large‐scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains	13
PDB‐tools web: A user‐friendly interface for the manipulation of PDB files	13
Identification of biochemically neutral positions in liver pyruvate kinase	13
High‐resolution structure of a partially folded insulin aggregation intermediate	13
Elucidating important structural features for the binding affinity of spike ‐ SARS‐CoV‐2 neutralizing antibody complexes	13
TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins	13
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling	13
Tertiary structure assessment at CASP15	12
Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction	12
A protein sequence fitness function for identifying natural and nonnatural proteins	12
Biological nanopores for sensing applications	12

Comparative protein structure network analysis on 3CLpro from SARS‐CoV‐1 and SARS‐CoV‐2	12
From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation	11
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments	11
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma	11
Genome‐wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights	11
Insights into the mechanisms of light‐oxygen‐voltage domain color tuning from a set of high‐resolution X‐ray structures	11
Using normal mode analysis on protein structural models. How far can we go on our predictions?	11
IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction	11
Critical assessment of methods of protein structure prediction (CASP)—Round XV	11
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots	11
Assessment of three‐dimensional RNA structure prediction in CASP15	11
Exploring the structure and dynamics of proteins in soil organic matter	10
Cryo‐EM targets in CASP14	10
RNA target highlights in CASP15: Evaluation of predicted models by structure providers	10
Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH	10
Assessing the binding properties of CASP14 targets and models	10
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images	9
Studying dynamics without explicit dynamics: A structure‐based study of the export mechanism by AcrB	9
Improved multimer prediction using massive sampling with AlphaFold in CASP15	9
Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation	9
Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker	9
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment	9
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses	9
A sequence‐based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum	9
Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution	9
An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions	9
Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)	9
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses	9
A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing	9
A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors	8
Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures	8
Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding	8
The effect of lipid composition on the dynamics of tau fibrils	8
Structural compliance: A new metric for protein flexibility	8
Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 2	8
DisCovER: distance‐ and orientation‐based covariational threading for weakly homologous proteins	8
Protein target highlights in CASP15: Analysis of models by structure providers	8
Expansin Engineering Database: A navigation and classification tool for expansins and homologues	8
Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes	8
Plastic structures for diverse substrates: A revisit of human ABC transporters	8
A rod conformation of the Pyrococcus furiosus Rad50 coiled coil	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
RNA tertiary structure modeling with BRiQ potential in CASP15	7
Protein structure search to support the development of protein structure prediction methods	7
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors	7
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring	7
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics study	7
Estimation of model accuracy in CASP15 using the ModFOLDdock server	7
In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms	7
Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model	7
Ca2+ as cofactor of the mitochondrial H+‐translocating F1FO‐ATP(hydrol)ase	7
Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin	7
A geometrical framework for thinking about proteins	6
VoroIF‐GNN: Voronoi tessellation‐derived protein–protein interface assessment using a graph neural network	6
RF‐SVM: Identification of DNA‐binding proteins based on comprehensive feature representation methods and support vector machine	6
Mapping of antibody epitopes based on docking and homology modeling	6
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts	6
Conserved internal hydration motifs in protein kinases	6
Performance of human and server prediction in CAPRI rounds 38‐45	6
Identification of key stabilizing interactions of amyloid‐β oligomers based on fragment molecular orbital calculations on macrocyclic β‐hairpin peptides	6
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces	6
Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15	6
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15	6
ANOVA‐particle swarm optimization‐based feature selection and gradient boosting machine classifier for improved protein–protein interaction prediction	6
Predicting mutant outcome by combining deep mutational scanning and machine learning	6
Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis	6
Circuit topology predicts pathogenicity of missense mutations	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
Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean	6
A detailed mapping of the readily accessible disulphide bonds in the cortex of wool fibres	6
Proteome analysis of the circadian clock protein PERIOD2	6
Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study	6
Can the jigsaw puzzle model of protein folding re‐assemble a hydrophobic core?	6
Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis	6
Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor	6
The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors	6
Calcium inhibits penetration of Alzheimer's Aβ1–42 monomers into the membrane	6
Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42	6
Structures of the TetR‐like transcription regulator RcdA alone and in complexes with ligands	6
Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions	6

Assessment of protein–ligand complexes in CASP15	6
Are granulins copper sequestering proteins?	6
Theoretical insights into molecular mechanism and energy criteria of PARP‐2 enzyme inhibition by benzimidazole analogues	6
N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study	6
The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils	6
Structures and interactions of insulin‐like peptides from cone snail venom	5
Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods	5
Tuning the binding interface between Machupo virus glycoprotein and human transferrin receptor	5
Further thermo‐stabilization of thermophilic rhodopsin from Thermus thermophilusJL‐18 through engineering in extramembrane regions	5
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors	5
From propensities to patterns to principles in protein folding	5
Protein folding and unfolding: proline cis‐trans isomerization at the c subunits of F1FO‐ATPase might open a high conductance ion channel	5
Distinctive communication networks in inactive states of β2‐adrenergic receptor: Mutual information and entropy transfer analysis	5
Sequence and evolutionary analysis of bacterial ribosomal S1 proteins	5
Catalytic and structural properties of ATP‐dependent caprolactamase from Pseudomonas jessenii	5
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery	5
Inhibition of Mycobacterium tuberculosisInhA by 3‐nitropropanoic acid	5
Surface salt bridges contribute to the extreme thermal stability of an FN3‐like domain from a thermophilic bacterium	5
Consistency and variation of protein subcellular location annotations	5
Simplified geometric representations of protein structures identify complementary interaction interfaces	5
Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers?	5
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps	5
Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation	5
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding	5
Conformational changes in a Vernier zone region: Implications for antibody dual specificity	5
Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B	5
Inferring metal binding sites in flexible regions of proteins	5
PeptiDesCalculator: Software for computation of peptide descriptors. Definition, implementation and case studies for 9 bioactivity endpoints	5
RNA tertiary structure prediction using RNAComposer in CASP15	5
Enhancing the promiscuity of a member of the Caspase protease family by rational design	5
Protein dynamics analysis identifies candidate cancer driver genes and mutations in TCGA data	5
Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide	5
How phosphorylation of peptides affects their interaction with 14‐3‐3η domains	5
Novel antimicrobial anionic cecropins from the spruce budworm feature a poly‐L‐aspartic acid C‐terminus	5
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks	5
Study on functional sites in human multidrug resistance protein 1 (hMRP1)	5
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane	5
Dihydrolipoamide dehydrogenase moonlighting activity as a DNA chelating agent	5
Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics simulations and graph machine learning	5
Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti‐cancer drug target	4
Design and characterization of a novel dimeric blood–brain barrier penetrating TNFα inhibitor	4
Structural evolution of the ancient enzyme, dissimilatory sulfite reductase	4
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid	4
Crystal‐structures‐guided design of fragment‐based drugs for inhibiting the main protease of SARS‐CoV‐2	4
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15	4
Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites	4
Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches	4
Remarked suppression of Aβ42 protomer–protomer dissociation reaction elucidated by molecular dynamics simulation	4
β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils	4
Crystal structure of Campylobacter jejuni lipoprotein Cj1090c	4
Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins	4
On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification	4
Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol‐phosphate dehydratase	4
New tyrosinases with putative action against contaminants of emerging concern	4
Substrate‐assisted activation and selectivity of the bacterial RavD effector deubiquitinylase	4
Analysis of CheW‐like domains provides insights into organization of prokaryotic chemotaxis systems	4
Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single‐particle cryo‐EM	4
Protein oligomer structure prediction using GALAXY in CASP14	4
The X‐ray crystal structure of human A15C neuroglobin reveals both native/de novo disulfide bonds and unexpected ligand‐binding sites	4
Predicting molecular properties of α‐synuclein using force fields for intrinsically disordered proteins	4
Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation	4
Identification of key molecular players and associated pathways in cervical squamous cell carcinoma progression through network analysis	4
The protonation state of Glu202 in acetylcholinesterase	4
Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites	4
Annexin A1, A2, A5, and A6 involvement in human pathologies	4
Dockground scoring benchmarks for protein docking	4
Role of conserved arginine in HadA monooxygenase for 4‐nitrophenol and 4‐chlorophenol detoxification	4
A new method for protein characterization and classification using geometrical features for 3D face analysis: An example of tubulin structures	4
Scaling‐up a fragment‐based protein–protein interaction method using a human reference interaction set	4
Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 α‐receptor	4
Common mechanism of thermostability in small α‐ and β‐proteins studied by molecular dynamics	4
Insights into modular polyketide synthase loops aided by repetitive sequences	4
CRMSNet: A deep learning model that uses convolution and residual multi‐head self‐attention block to predict RBPs for RNA sequence	4
A Maximum Caliber analysis of the Foldon Hypothesis	4
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15	4
Introduction of a new scheme for classifying β‐turns in protein structures	4
SCLpred‐MEM: Subcellular localization prediction of membrane proteins by deep N‐to‐1 convolutional neural networks	4
Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase	4
Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis	4
Antibody mutations favoring pH‐dependent binding in solid tumor microenvironments: Insights from large‐scale structure‐based calculations	4
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15	4
MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH	4
Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior	4
II. Geometrical framework for thinking about globular proteins: The power of poking	4
Influence of electrostatic forces on the association kinetics and conformational ensemble of an intrinsically disordered protein	4
Crystal structure of a S‐adenosyl‐L‐methionine‐dependent O‐methyltransferase‐like enzyme from Aspergillus flavus	4
Assessment of the assessment—All about complexes	4
Total free energy analysis of fully hydrated proteins	4