| 1 | NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids | 15.5 | 16 | Citations (PDF) |
| 2 | Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites | 15.5 | 13 | Citations (PDF) |
| 3 | DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach | 15.5 | 7 | Citations (PDF) |
| 4 | Determining the effects of pseudouridine incorporation on human tRNAs | 7.3 | 14 | Citations (PDF) |
| 5 | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations | 8.1 | 5 | Citations (PDF) |
| 6 | Modeling flexible RNA 3D structures and RNA-protein complexes | 6.4 | 7 | Citations (PDF) |
| 7 | MODOMICS: a database of RNA modifications and related information. 2023 update | 15.5 | 415 | Citations (PDF) |
| 8 | Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology | 4.1 | 10 | Citations (PDF) |
| 9 | Conserved structures and dynamics in 5′-proximal regions of Betacoronavirus RNA genomes | 15.5 | 17 | Citations (PDF) |
| 10 | DEGRONOPEDIA: a web server for proteome-wide inspection of degrons | 15.5 | 34 | Citations (PDF) |
| 11 | SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories | 15.5 | 30 | Citations (PDF) |
| 12 | Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens | 3.5 | 12 | Citations (PDF) |
| 13 | ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment | 15.5 | 5 | Citations (PDF) |
| 14 | Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data | 3.8 | 31 | Citations (PDF) |
| 15 | The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among m6A core genes | 2.8 | 7 | Citations (PDF) |
| 16 | Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold | 4.1 | 6 | Citations (PDF) |
| 17 | NACDDB: Nucleic Acid Circular Dichroism Database | 15.5 | 27 | Citations (PDF) |
| 18 | 1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes | 5.9 | 6 | Citations (PDF) |
| 19 | Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA | 6.6 | 31 | Citations (PDF) |
| 20 | RNA target highlights in CASP15: Evaluation of predicted models by structure providers | 2.6 | 49 | Citations (PDF) |
| 21 | RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints | 2.6 | 11 | Citations (PDF) |
| 22 | RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints | 4.7 | 14 | Citations (PDF) |
| 23 | A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures | 15.5 | 17 | Citations (PDF) |
| 24 | MODOMICS: a database of RNA modification pathways. 2021 update | 15.5 | 798 | Citations (PDF) |
| 25 | DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes | 15.5 | 18 | Citations (PDF) |
| 26 | Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26 | 2.6 | 8 | Citations (PDF) |
| 27 | fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions | 3.1 | 29 | Citations (PDF) |
| 28 | Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models | 4.4 | 29 | Citations (PDF) |
| 29 | DNAmoreDB, a database of DNAzymes | 15.5 | 40 | Citations (PDF) |
| 30 | AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses | 3.1 | 83 | Citations (PDF) |
| 31 | RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity | 5.5 | 21 | Citations (PDF) |
| 32 | Constrained peptides mimic a viral suppressor of RNA silencing | 15.5 | 21 | Citations (PDF) |
| 33 | A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair | 2.5 | 18 | Citations (PDF) |
| 34 | Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements | 15.5 | 300 | Citations (PDF) |
| 35 | RNAProbe: a web server for normalization and analysis of RNA structure probing data | 15.5 | 25 | Citations (PDF) |
| 36 | RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers | 3.8 | 167 | Citations (PDF) |
| 37 | RNA 3D structure prediction guided by independent folding of homologous sequences | 3.0 | 27 | Citations (PDF) |
| 38 | Petri net–based model of the human DNA base excision repair pathway | 2.3 | 5 | Citations (PDF) |
| 39 | Matching tRNA modifications in humans to their known and predicted enzymes | 15.5 | 168 | Citations (PDF) |
| 40 | Computational modeling of RNA 3D structure based on experimental data | 3.8 | 57 | Citations (PDF) |
| 41 | Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com | 2.3 | 8 | Citations (PDF) |
| 42 | Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease | 4.1 | 3 | Citations (PDF) |
| 43 | Structural bases of peptidoglycan recognition by lysostaphin SH3b domain | 3.4 | 94 | Citations (PDF) |
| 44 | RRMdb—an evolutionary-oriented database of RNA recognition motif sequences | 2.7 | 12 | Citations (PDF) |
| 45 | Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition | 13.7 | 53 | Citations (PDF) |
| 46 | MODOMICS: a database of RNA modification pathways. 2017 update | 15.5 | 1,704 | Citations (PDF) |
| 47 | Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics | 5.3 | 20 | Citations (PDF) |
| 48 | Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini | 3.7 | 28 | Citations (PDF) |
| 49 | Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes | 2.5 | 47 | Citations (PDF) |
| 50 | RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme | 3.8 | 198 | Citations (PDF) |
| 51 | Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates | 2.2 | 40 | Citations (PDF) |
| 52 | Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods | 3.5 | 46 | Citations (PDF) |
| 53 | Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro | 3.4 | 9 | Citations (PDF) |
| 54 | Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs | 15.5 | 65 | Citations (PDF) |
| 55 | SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments | 15.5 | 13 | Citations (PDF) |
| 56 | Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition | 2.3 | 24 | Citations (PDF) |
| 57 | Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases | 3.4 | 12 | Citations (PDF) |
| 58 | Coarse-grained modeling of RNA 3D structure | 3.5 | 63 | Citations (PDF) |
| 59 | SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction | 15.5 | 434 | Citations (PDF) |
| 60 | SimRNAweb: a web server for RNA 3D structure modeling with optional restraints | 15.5 | 134 | Citations (PDF) |
| 61 | Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase | 2.9 | 5 | Citations (PDF) |
| 62 | tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs | 3.5 | 12 | Citations (PDF) |
| 63 | Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts | 2.4 | 12 | Citations (PDF) |
| 64 | Computational modeling of RNA 3D structures and interactions | 6.4 | 50 | Citations (PDF) |
| 65 | Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue | 15.5 | 36 | Citations (PDF) |
| 66 | The architecture of the Schizosaccharomyces pombe CCR4-NOT complex | 13.7 | 56 | Citations (PDF) |
| 67 | Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species,<i>Helicobacter pylori</i> | 2.8 | 8 | Citations (PDF) |
| 68 | Sequence-specific cleavage of dsRNA by Mini-III RNase | 15.5 | 32 | Citations (PDF) |
| 69 | Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes | 3.0 | 47 | Citations (PDF) |
| 70 | Modeling of ribonucleic acid–ligand interactions | 18.7 | 18 | Citations (PDF) |
| 71 | Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631 | 2.3 | 58 | Citations (PDF) |
| 72 | Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection | 15.5 | 121 | Citations (PDF) |
| 73 | An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies | 15.5 | 21 | Citations (PDF) |
| 74 | The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein | 4.1 | 29 | Citations (PDF) |
| 75 | Brickworxbuilds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps | 3.1 | 16 | Citations (PDF) |
| 76 | Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2′ 5′-oligoadenylate synthetase family | 2.3 | 26 | Citations (PDF) |
| 77 | RNAcentral: an international database of ncRNA sequences | 15.5 | 122 | Citations (PDF) |
| 78 | An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies | 15.5 | 66 | Citations (PDF) |
| 79 | NPDock: a web server for protein–nucleic acid docking | 15.5 | 236 | Citations (PDF) |
| 80 | GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function | 4.7 | 39 | Citations (PDF) |
| 81 | Structure and intrinsic disorder of the proteins of the<i>Trypanosoma brucei</i> editosome | 2.7 | 7 | Citations (PDF) |
| 82 | RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures | 3.8 | 196 | Citations (PDF) |
| 83 | Distribution and frequencies of post-transcriptional modifications in tRNAs | 3.3 | 202 | Citations (PDF) |
| 84 | RNA methyltransferases involved in 5′ cap biosynthesis | 3.3 | 89 | Citations (PDF) |
| 85 | Computational modeling of RNA 3D structures, with the aid of experimental restraints | 3.3 | 40 | Citations (PDF) |
| 86 | Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation | 13.7 | 101 | Citations (PDF) |
| 87 | CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction | 15.5 | 17 | Citations (PDF) |
| 88 | RNA Bricks—a database of RNA 3D motifs and their interactions | 15.5 | 99 | Citations (PDF) |
| 89 | Structural basis of the methylation specificity of R.DpnI | 15.5 | 39 | Citations (PDF) |
| 90 | ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes | 15.5 | 58 | Citations (PDF) |
| 91 | The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification | 15.5 | 169 | Citations (PDF) |
| 92 | Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR | 2.3 | 23 | Citations (PDF) |
| 93 | Computational modeling of protein–RNA complex structures | 3.5 | 32 | Citations (PDF) |
| 94 | Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures | 2.3 | 19 | Citations (PDF) |
| 95 | Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production | 4.3 | 6 | Citations (PDF) |
| 96 | Functional and Bioinformatics Analysis of Two Campylobacter jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA | 2.3 | 21 | Citations (PDF) |
| 97 | Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid | 15.5 | 52 | Citations (PDF) |
| 98 | S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA | 3.8 | 23 | Citations (PDF) |
| 99 | LigandRNA: computational predictor of RNA–ligand interactions | 3.8 | 100 | Citations (PDF) |
| 100 | CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction | 15.5 | 113 | Citations (PDF) |
| 101 | QA-RecombineIt: a server for quality assessment and recombination of protein models | 15.5 | 10 | Citations (PDF) |
| 102 | RNAlyzer—novel approach for quality analysis of RNA structural models | 15.5 | 26 | Citations (PDF) |
| 103 | Crystal structures of the tRNA:m 2 G6 methyltransferase Trm14/TrmN from two domains of life | 15.5 | 47 | Citations (PDF) |
| 104 | Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation | 4.7 | 24 | Citations (PDF) |
| 105 | MetalionRNA: computational predictor of metal-binding sites in RNA structures | 4.7 | 51 | Citations (PDF) |
| 106 | RNApathwaysDB—a database of RNA maturation and decay pathways | 15.5 | 10 | Citations (PDF) |
| 107 | Rational engineering of sequence specificity in R.MwoI restriction endonuclease | 15.5 | 3 | Citations (PDF) |
| 108 | Structural bioinformatics of the human spliceosomal proteome | 15.5 | 44 | Citations (PDF) |
| 109 | Sequence-specific cleavage of the RNA strand in DNA–RNA hybrids by the fusion of ribonuclease H with a zinc finger | 15.5 | 20 | Citations (PDF) |
| 110 | MODOMICS: a database of RNA modification pathways—2013 update | 15.5 | 1,000 | Citations (PDF) |
| 111 | RNA-Puzzles
: A CASP-like evaluation of RNA three-dimensional structure prediction | 3.8 | 303 | Citations (PDF) |
| 112 | The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA | 3.8 | 22 | Citations (PDF) |
| 113 | RIBER/DIBER: a software suite for crystal content analysis in the studies of protein–nucleic acid complexes | 4.7 | 5 | Citations (PDF) |
| 114 | Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII | 15.5 | 18 | Citations (PDF) |
| 115 | Structure of eukaryotic 2′-O-ribose methyltransferase in complex with mRNA cap analogue | 0.2 | 0 | Citations (PDF) |
| 116 | Computational methods for prediction of protein–RNA interactions | 2.3 | 125 | Citations (PDF) |
| 117 | Statins Impair Glucose Uptake in Tumor Cells | 7.0 | 39 | Citations (PDF) |
| 118 | Novel non-specific DNA adenine methyltransferases | 15.5 | 64 | Citations (PDF) |
| 119 | Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI | 15.5 | 62 | Citations (PDF) |
| 120 | MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins | 3.0 | 315 | Citations (PDF) |
| 121 | Molecular evolution of dihydrouridine synthases | 3.0 | 39 | Citations (PDF) |
| 122 | The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement | 3.0 | 10 | Citations (PDF) |
| 123 | Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities | 4.0 | 21 | Citations (PDF) |
| 124 | MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria | 2.0 | 29 | Citations (PDF) |
| 125 | A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome | 3.0 | 34 | Citations (PDF) |
| 126 | Intrinsic Disorder in the Human Spliceosomal Proteome | 3.1 | 85 | Citations (PDF) |
| 127 | A toolbox for developing bioinformatics software | 6.6 | 20 | Citations (PDF) |
| 128 | REPAIRtoire--a database of DNA repair pathways | 15.5 | 64 | Citations (PDF) |
| 129 | STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNγ, TLR4 and IL-6 in vascular disease | 10.5 | 103 | Citations (PDF) |
| 130 | Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase | 13.3 | 0 | Citations (PDF) |
| 131 | REVIEW PAPER<BR>Virtual screening strategies in drug design
– methods and applications | 2.0 | 46 | Citations (PDF) |
| 132 | Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed byTrypanosoma bruceisterol C-24-methyltransferase | 3.8 | 12 | Citations (PDF) |
| 133 | RNA tertiary structure prediction with ModeRNA | 6.6 | 18 | Citations (PDF) |
| 134 | RNA and protein 3D structure modeling: similarities and differences | 2.3 | 86 | Citations (PDF) |
| 135 | ModeRNA: a tool for comparative modeling of RNA 3D structure | 15.5 | 289 | Citations (PDF) |
| 136 | Evidence for an evolutionary antagonism between Mrr and Type III modification systems | 15.5 | 27 | Citations (PDF) |
| 137 | Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit | 15.5 | 32 | Citations (PDF) |
| 138 | A Single Zinc Ion Is Sufficient for an Active Trypanosoma brucei tRNA Editing Deaminase | 2.2 | 19 | Citations (PDF) |
| 139 | 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family | 15.5 | 153 | Citations (PDF) |
| 140 | ModeRNA server: an online tool for modeling RNA 3D structures | 4.7 | 65 | Citations (PDF) |
| 141 | Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair | 4.5 | 65 | Citations (PDF) |
| 142 | Physiological truncation and domain organization of a novel uracil‐DNA‐degrading factor | 5.3 | 5 | Citations (PDF) |
| 143 | Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m 7 G methyltransferases | 15.5 | 39 | Citations (PDF) |
| 144 | New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA | 15.5 | 50 | Citations (PDF) |
| 145 | FILTREST3D: discrimination of structural models using restraints from experimental data | 4.7 | 21 | Citations (PDF) |
| 146 | Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria | 15.5 | 82 | Citations (PDF) |
| 147 | A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI) | 15.5 | 14 | Citations (PDF) |
| 148 | Predicting Atomic Details of the Unfolding Pathway for YibK, a Knotted Protein from the SPOUT Superfamily | 2.6 | 36 | Citations (PDF) |
| 149 | The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket | 2.3 | 21 | Citations (PDF) |
| 150 | Crystal structure of a fructokinase homolog from Halothermothrix orenii | 2.3 | 21 | Citations (PDF) |
| 151 | Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors | 1.8 | 25 | Citations (PDF) |
| 152 | The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein | 15.5 | 85 | Citations (PDF) |
| 153 | SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes | 4.6 | 42 | Citations (PDF) |
| 154 | Identification and Classification ofbclGenes and Proteins ofBacillus cereusGroup Organisms and Their Application inBacillus anthracisDetection and Fingerprinting | 3.6 | 42 | Citations (PDF) |
| 155 | MODOMICS: a database of RNA modification pathways. 2008 update | 15.5 | 190 | Citations (PDF) |
| 156 | Functional Analysis of MmeI from Methanol UtilizerMethylophilus methylotrophus, a Subtype IIC Restriction-Modification Enzyme Related to Type I Enzymes | 3.6 | 20 | Citations (PDF) |
| 157 | Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family | 4.0 | 24 | Citations (PDF) |
| 158 | YgdE is the 2′‐O‐ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA | 2.5 | 70 | Citations (PDF) |
| 159 | Integrating
ELF4
into the circadian system through combined structural and functional studies | 2.2 | 109 | Citations (PDF) |
| 160 | Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase | 13.3 | 85 | Citations (PDF) |
| 161 | Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure | 5.9 | 14 | Citations (PDF) |
| 162 | Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site | 1.8 | 15 | Citations (PDF) |
| 163 | Sequence–structure–function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA | 2.6 | 19 | Citations (PDF) |
| 164 | Virtual Screening and Experimental Verification to Identify Potential Inhibitors of the ErmC Methyltransferase Responsible for Bacterial Resistance against Macrolide Antibiotics | 3.1 | 35 | Citations (PDF) |
| 165 | Structural integrity of the Beta Beta Alpha-Metal finger motif is required for DNA binding and stable protein–DNA complex formation in R.KpnI | 2.0 | 5 | Citations (PDF) |
| 166 | Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm | 2.0 | 20 | Citations (PDF) |
| 167 | Pcons: A neural-network-based consensus predictor that improves fold recognition | 5.9 | 207 | Citations (PDF) |
| 168 | Predicting the Complex Structure and Functional Motions of the Outer Membrane Transporter and Signal Transducer FecA | 2.2 | 11 | Citations (PDF) |
| 169 | Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases | 12.2 | 50 | Citations (PDF) |
| 170 | HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling | 4.1 | 32 | Citations (PDF) |
| 171 | The PMS2 Subunit of Human MutLα Contains a Metal Ion Binding Domain of the Iron-Dependent Repressor Protein Family | 4.1 | 57 | Citations (PDF) |
| 172 | YccW is the m5C Methyltransferase Specific for 23S rRNA Nucleotide 1962 | 4.1 | 62 | Citations (PDF) |
| 173 | Crystal Structure of the Escherichia coli 23S rRNA:m5C Methyltransferase RlmI (YccW) Reveals Evolutionary Links between RNA Modification Enzymes | 4.1 | 39 | Citations (PDF) |
| 174 | Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr | 2.1 | 13 | Citations (PDF) |
| 175 | Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily | 3.2 | 22 | Citations (PDF) |
| 176 | Bud23 Methylates G1575 of 18S rRNA and Is Required for Efficient Nuclear Export of Pre-40S Subunits | 2.5 | 127 | Citations (PDF) |
| 177 | The YqfN protein of Bacillus subtilis is the tRNA: m 1 A22 methyltransferase (TrmK) | 15.5 | 37 | Citations (PDF) |
| 178 | EXOG, a novel paralog of Endonuclease G in higher eukaryotes | 15.5 | 74 | Citations (PDF) |
| 179 | Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses | 15.5 | 114 | Citations (PDF) |
| 180 | YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA | 3.8 | 69 | Citations (PDF) |
| 181 | The Structure of Sucrose Phosphate Synthase from Halothermothrix orenii Reveals Its Mechanism of Action and Binding Mode
| 7.6 | 57 | Citations (PDF) |
| 182 | The TbMTr1 Spliced Leader RNA Cap 1 2 ′-O-Ribose Methyltransferase from Trypanosoma brucei Acts with Substrate Specificity | 2.2 | 22 | Citations (PDF) |
| 183 | Modeling of Escherichia coli Endonuclease V structure in complex with DNA | 2.3 | 4 | Citations (PDF) |
| 184 | Human lysosomal DNase II contains two requisite PLD-signature (HxK) motifs: Evidence for a pseudodimeric structure of the active enzyme species | 5.9 | 30 | Citations (PDF) |
| 185 | Conserved amino acids in each subunit of the heteroligomeric tRNA m 1 A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding | 15.5 | 35 | Citations (PDF) |
| 186 | PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure | 4.7 | 25 | Citations (PDF) |
| 187 | Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC | 15.5 | 31 | Citations (PDF) |
| 188 | I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition | 4.7 | 36 | Citations (PDF) |
| 189 | Novel protein fold discovered in the PabI family of restriction enzymes | 15.5 | 49 | Citations (PDF) |
| 190 | Identification of a Missing Sequence and Functionally Important Residues of 16S rRNA:m1A1408 Methyltransferase KamB that Causes Bacterial Resistance to Aminoglycoside Antibiotics | 3.2 | 11 | Citations (PDF) |
| 191 | The 2′-
O
-Ribose Methyltransferase for Cap 1 of Spliced Leader RNA and U1 Small Nuclear RNA in
Trypanosoma brucei | 2.5 | 22 | Citations (PDF) |
| 192 | Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I | 4.1 | 23 | Citations (PDF) |
| 193 | Structure of a Multipartite Protein-Protein Interaction Domain in Splicing Factor Prp8 and Its Link to Retinitis Pigmentosa | 13.3 | 126 | Citations (PDF) |
| 194 | Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily | 1.8 | 37 | Citations (PDF) |
| 195 | Phylogenetic analysis of haloalkane dehalogenases | 2.6 | 87 | Citations (PDF) |
| 196 | A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering | 2.6 | 14 | Citations (PDF) |
| 197 | Probing of contacts between EcoRII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling | 0.8 | 1 | Citations (PDF) |
| 198 | Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases | 3.0 | 163 | Citations (PDF) |
| 199 | SURF’s UP! — Protein classification by surface comparisons | 1.4 | 15 | Citations (PDF) |
| 200 | Structure and Evolutionary Origin of Ca2+-Dependent Herring Type II Antifreeze Protein | 2.3 | 70 | Citations (PDF) |
| 201 | Importance of local model quality in molecular replacement method | 0.2 | 0 | Citations (PDF) |
| 202 | Evaluation of Molecular Models for the Affinity Maturation of Antibodies: Roles of Cytosine Deamination by AID and DNA Repair | 52.5 | 31 | Citations (PDF) |
| 203 | Characterization of prmt7α and β isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors | 2.0 | 32 | Citations (PDF) |
| 204 | Helicobacter pylori protein oxidation influences the colonization process | 2.8 | 25 | Citations (PDF) |
| 205 | Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI | 15.5 | 17 | Citations (PDF) |
| 206 | Title is missing! | 4.0 | 51 | Citations (PDF) |
| 207 | Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis | 2.6 | 8 | Citations (PDF) |
| 208 | Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease | 2.6 | 27 | Citations (PDF) |
| 209 | Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length | 2.0 | 12 | Citations (PDF) |
| 210 | Title is missing! | 3.1 | 49 | Citations (PDF) |
| 211 | Phylogenomic analysis of the GIY-YIG nuclease superfamily | 3.2 | 128 | Citations (PDF) |
| 212 | Protein-Structure Prediction by Recombination of Fragments | 2.6 | 85 | Citations (PDF) |
| 213 | THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain | 15.5 | 29 | Citations (PDF) |
| 214 | Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase | 15.5 | 37 | Citations (PDF) |
| 215 | Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA | 15.5 | 22 | Citations (PDF) |
| 216 | Complete Cap 4 Formation Is Not Required for Viability in
Trypanosoma brucei | 2.7 | 33 | Citations (PDF) |
| 217 | The Yeast Arr4p ATPase Binds the Chloride Transporter Gef1p When Copper Is Available in the Cytosol | 2.2 | 44 | Citations (PDF) |
| 218 | Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase | 2.1 | 13 | Citations (PDF) |
| 219 | MODOMICS: a database of RNA modification pathways | 15.5 | 261 | Citations (PDF) |
| 220 | Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface | 2.6 | 6 | Citations (PDF) |
| 221 | Theoretical predictions of the impact of the trisubstituted pyrophosphate internucleotide bond on B DNA fragments | 1.2 | 0 | Citations (PDF) |
| 222 | Title is missing! | 3.0 | 101 | Citations (PDF) |
| 223 | Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site | 3.2 | 38 | Citations (PDF) |
| 224 | Title is missing! | 1.8 | 19 | Citations (PDF) |
| 225 | Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis | 2.6 | 32 | Citations (PDF) |
| 226 | Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA | 2.5 | 113 | Citations (PDF) |
| 227 | Specificity Changes in the Evolution of Type II Restriction Endonucleases | 2.2 | 32 | Citations (PDF) |
| 228 | Mva1269I: A Monomeric Type IIS Restriction Endonuclease from Micrococcus Varians with Two EcoRI- and FokI-like Catalytic Domains | 2.2 | 26 | Citations (PDF) |
| 229 | DNase II is a member of the phospholipase D superfamily | 4.7 | 13 | Citations (PDF) |
| 230 | A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy | 2.6 | 14 | Citations (PDF) |
| 231 | Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII | 15.5 | 18 | Citations (PDF) |
| 232 | Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi | 15.5 | 89 | Citations (PDF) |
| 233 | Molecular modelling of a psychrophilic β-galactosidase | 1.9 | 6 | Citations (PDF) |
| 234 | Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII | 3.1 | 15 | Citations (PDF) |
| 235 | Analysis of the Quaternary Structure of the MutL C-terminal Domain | 4.1 | 56 | Citations (PDF) |
| 236 | N2-Methylation of Guanosine at Position 10 in tRNA Is Catalyzed by a THUMP Domain-containing, S-Adenosylmethionine-dependent Methyltransferase, Conserved in Archaea and Eukaryota | 2.2 | 70 | Citations (PDF) |
| 237 | COLORADO3D, a web server for the visual analysis of protein structures | 15.5 | 55 | Citations (PDF) |
| 238 | A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase | 15.5 | 120 | Citations (PDF) |
| 239 | Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases | 15.5 | 101 | Citations (PDF) |
| 240 | Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily | 15.5 | 81 | Citations (PDF) |
| 241 | Homology Modeling of the CG-specific DNA Methyltransferase SssI and its Complexes with DNA and AdoHcy | 2.6 | 25 | Citations (PDF) |
| 242 | Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC′ | 2.9 | 4 | Citations (PDF) |
| 243 | Sterol Methyltransferase: Functional Analysis of Highly Conserved Residues by Site-Directed Mutagenesis | 2.4 | 38 | Citations (PDF) |
| 244 | Structural and Functional Characterization of Mitochondrial EndoG, a Sugar Non-specific Nuclease which Plays an Important Role During Apoptosis | 4.1 | 95 | Citations (PDF) |
| 245 | Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB | 3.2 | 200 | Citations (PDF) |
| 246 | Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii | 2.6 | 2 | Citations (PDF) |
| 247 | Structure, evolution, and inhibitor interaction of S‐adenosyl‐L‐homocysteine hydrolase from Plasmodium falciparum | 2.6 | 40 | Citations (PDF) |
| 248 | Experimental Evidence for a ββα-Me-Finger Nuclease Motif To Represent the Active Site of the Caspase-Activated DNase† | 2.4 | 23 | Citations (PDF) |
| 249 | GeneSilico protein structure prediction meta-server | 15.5 | 407 | Citations (PDF) |
| 250 | Title is missing! | 3.0 | 15 | Citations (PDF) |
| 251 | Topological Measurement of an A-tract Bend Angle: Comparison of the Bent and Straightened States | 4.1 | 21 | Citations (PDF) |
| 252 | PspGI, a Type II Restriction Endonuclease from the Extreme Thermophile Pyrococcus sp.: Structural and Functional Studies to Investigate an Evolutionary Relationship with Several Mesophilic Restriction Enzymes | 4.1 | 49 | Citations (PDF) |
| 253 | Mutational Analysis Defines the Roles of Conserved Amino Acid Residues in the Predicted Catalytic Pocket of the rRNA:m6A Methyltransferase ErmC′ | 4.1 | 40 | Citations (PDF) |
| 254 | Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2′-O-methyltransferases | 2.3 | 107 | Citations (PDF) |
| 255 | STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification | 4.7 | 8 | Citations (PDF) |
| 256 | Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase | 15.5 | 52 | Citations (PDF) |
| 257 | The
yggH
Gene of
Escherichia coli
Encodes a tRNA (m
7
G46) Methyltransferase | 2.9 | 81 | Citations (PDF) |
| 258 | Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures | 15.5 | 107 | Citations (PDF) |
| 259 | Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions | 15.5 | 48 | Citations (PDF) |
| 260 | ORFeus: detection of distant homology using sequence profiles and predicted secondary structure | 15.5 | 118 | Citations (PDF) |
| 261 | Evolutionary Relationship between Different Subgroups of Restriction Endonucleases | 2.2 | 53 | Citations (PDF) |
| 262 | In silico identification, structure prediction and phylogenetic analysis of the 2′-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses | 2.6 | 72 | Citations (PDF) |
| 263 | Streptococcal Scl1 and Scl2 Proteins Form Collagen-like Triple Helices | 2.2 | 187 | Citations (PDF) |
| 264 | Fold-recognition detects an error in the Protein Data Bank | 4.7 | 20 | Citations (PDF) |
| 265 | Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases | 2.5 | 6 | Citations (PDF) |
| 266 | Title is missing! | 3.0 | 30 | Citations (PDF) |
| 267 | Title is missing! | 3.1 | 65 | Citations (PDF) |
| 268 | Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for Malaria and Leishmaniasis | 10.8 | 72 | Citations (PDF) |
| 269 | Structure Prediction and Phylogenetic Analysis of a Functionally Diverse Family of Proteins Homologous to the MT-A70 Subunit of the Human mRNA:m6A Methyltransferase | 1.7 | 210 | Citations (PDF) |
| 270 | MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase | 7.3 | 84 | Citations (PDF) |
| 271 | Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop | 7.3 | 163 | Citations (PDF) |
| 272 | Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases | 5.9 | 17 | Citations (PDF) |
| 273 | Title is missing! | 12.2 | 48 | Citations (PDF) |
| 274 | Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs | 2.3 | 40 | Citations (PDF) |
| 275 | In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea | 2.7 | 39 | Citations (PDF) |
| 276 | LiveBench-2: Large-scale automated evaluation of protein structure prediction servers | 2.6 | 68 | Citations (PDF) |
| 277 | Title is missing! 2001, 22, 219-230 | | 36 | Citations (PDF) |
| 278 | LiveBench-1: Continuous benchmarking of protein structure prediction servers | 5.9 | 136 | Citations (PDF) |
| 279 | Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed | 6.7 | 70 | Citations (PDF) |
| 280 | Title is missing! | 3.0 | 26 | Citations (PDF) |
| 281 | Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY–YIG superfamily member, using NMR restraints and Monte Carlo dynamics | 2.6 | 16 | Citations (PDF) |
| 282 | Structure prediction meta server | 4.7 | 218 | Citations (PDF) |
| 283 | Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases | 2.5 | 25 | Citations (PDF) |
| 284 | Phylogeny of the Restriction Endonuclease-Like Superfamily Inferred from Comparison of Protein Structures | 1.7 | 77 | Citations (PDF) |
| 285 | Phylogenomic analysis of 16S rRNA:(guanine‐N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino‐methyltransferases | 0.6 | 45 | Citations (PDF) |
| 286 | Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases? | 8.1 | 7 | Citations (PDF) |
| 287 | Is the HemK Family of Putative S-Adenosylmethionine-Dependent Methyltransferases a "Missing" zeta Subfamily of Adenine Methyltransferases? A Hypothesis | 2.9 | 17 | Citations (PDF) |
| 288 | RNArchitecture: a database and a classification system of RNA families, with a focus on structural information | 15.5 | 33 | Citations (PDF) |
| 289 | The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity | 15.5 | 8 | Citations (PDF) |
| 290 | RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools | 15.5 | 58 | Citations (PDF) |
| 291 | A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing | 0.7 | 34 | Citations (PDF) |
| 292 | Crystal structure of human Acinus RNA recognition motif domain | 0.0 | 3 | Citations (PDF) |
| 293 | Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles | 8.8 | 5 | Citations (PDF) |
| 294 | Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures | 3.4 | 2 | Citations (PDF) |
| 295 | Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders | 6.6 | 0 | Citations (PDF) |
| 296 | MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary | 15.5 | 36 | Citations (PDF) |
| 297 | ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment | 15.5 | 1 | Citations (PDF) |
