| 1 | PANDA: PAN Cancer Data Analysis Web Tool | 3.0 | 7 | Citations (PDF) |
| 2 | BEAGLE 2.0: A Web Server for RNA Secondary Structure Similarity Detection Leveraging SHAPE-directed RNA Structure Determination | 3.0 | 2 | Citations (PDF) |
| 3 | Integrating gene expression, genomic, and phosphoproteomic data to infer transcription factor activity in lung cancer | 1.4 | 0 | Citations (PDF) |
| 4 | LEADR, a p63 target, dampens interferon signalling in bladder cancer | 5.6 | 6 | Citations (PDF) |
| 5 | Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction | 1.0 | 4 | Citations (PDF) |
| 6 | NRF2 connects Src tyrosine kinase to ferroptosis resistance in glioblastoma | 1.9 | 29 | Citations (PDF) |
| 7 | A Meta-Analysis Approach to Gene Regulatory Network Inference Identifies Key Regulators of Cardiovascular Diseases | 3.2 | 6 | Citations (PDF) |
| 8 | Human lncRNAs harbor conserved modules embedded in different sequence contexts | 3.4 | 3 | Citations (PDF) |
| 9 | Looking for Plant microRNAs in Human Blood Samples: Bioinformatics Evidence and Perspectives | 2.0 | 17 | Citations (PDF) |
| 10 | Exploring the landscape of tools and resources for the analysis of long non-coding RNAs | 2.7 | 15 | Citations (PDF) |
| 11 | PDBe-KB: collaboratively defining the biological context of structural data | 11.2 | 89 | Citations (PDF) |
| 12 | Evaluation of potential miRNA sponge effects of SARS genomes in human | 3.4 | 12 | Citations (PDF) |
| 13 | Conserved exchange of paralog proteins during neuronal differentiation | 1.9 | 2 | Citations (PDF) |
| 14 | Variation in the co-expression profile highlights a loss of miRNA-mRNA regulation in multiple cancer types | 3.4 | 3 | Citations (PDF) |
| 15 | Artificial intelligence methods enhance the discovery of RNA interactions | 2.4 | 14 | Citations (PDF) |
| 16 | Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments | 1.4 | 4 | Citations (PDF) |
| 17 | BRIO: a web server for RNA sequence and structure motif scan | 11.2 | 21 | Citations (PDF) |
| 18 | Variants in MHY7 Gene Cause Arrhythmogenic Cardiomyopathy | 1.8 | 7 | Citations (PDF) |
| 19 | A eutherian-specific microRNA controls the translation of Satb2 in a model of cortical differentiation | 3.0 | 18 | Citations (PDF) |
| 20 | COTAN: scRNA-seq data analysis based on gene co-expression | 1.4 | 24 | Citations (PDF) |
| 21 | Early life adversity affecting the attachment bond alters ventral tegmental area transcriptomic patterning and behavior almost exclusively in female mice | 2.4 | 12 | Citations (PDF) |
| 22 | PDBe-KB: a community-driven resource for structural and functional annotations | 11.2 | 134 | Citations (PDF) |
| 23 | COVID-19 and Genetic Variants of Protein Involved in the SARS-CoV-2 Entry into the Host Cells | 1.8 | 100 | Citations (PDF) |
| 24 | RISC RNA sequencing in the Dorsal Raphè reveals microRNAs regulatory activities associated with behavioral and functional adaptations to chronic stress | 1.9 | 6 | Citations (PDF) |
| 25 | A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) | 0.3 | 17 | Citations (PDF) |
| 26 | Kinome-wide identification of phosphorylation networks in eukaryotic proteomes | 3.2 | 62 | Citations (PDF) |
| 27 | Modeling cancer drug response through drug-specific informative genes | 2.7 | 60 | Citations (PDF) |
| 28 | Discovering sequence and structure landscapes in RNA interaction motifs | 11.2 | 23 | Citations (PDF) |
| 29 | BEAM web server: a tool for structural RNA motif discovery | 3.2 | 14 | Citations (PDF) |
| 30 | Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells | 2.2 | 35 | Citations (PDF) |
| 31 | A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications | 11.2 | 22 | Citations (PDF) |
| 32 | The human rs1050286 polymorphism alters LOX‐1 expression through modifying miR‐24 binding | 2.4 | 23 | Citations (PDF) |
| 33 | Revealing protein–lncRNA interaction | 4.0 | 654 | Citations (PDF) |
| 34 | Tools and data services registry: a community effort to document bioinformatics resources | 11.2 | 145 | Citations (PDF) |
| 35 | Web-Beagle: a web server for the alignment of RNA secondary structures: Figure 1. | 11.2 | 39 | Citations (PDF) |
| 36 | Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling | 23.8 | 189 | Citations (PDF) |
| 37 | Exploiting holistic approaches to model specificity in protein phosphorylation | 1.6 | 14 | Citations (PDF) |
| 38 | Computational methods for analysis and inference of kinase/inhibitor relationships | 1.6 | 18 | Citations (PDF) |
| 39 | A Proteome-wide Domain-centric Perspective on Protein Phosphorylation | 3.5 | 6 | Citations (PDF) |
| 40 | A novel approach to represent and compare RNA secondary structures | 11.2 | 52 | Citations (PDF) |
| 41 | Regulation Dynamics of Leishmania Differentiation: Deconvoluting Signals and Identifying Phosphorylation Trends | 3.5 | 78 | Citations (PDF) |
| 42 | AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation | 12.8 | 235 | Citations (PDF) |
| 43 | Bioinformatics in Italy: BITS2012, the ninth annual meeting of the Italian Society of Bioinformatics | 2.5 | 1 | Citations (PDF) |
| 44 | Alternative splicing tends to avoid partial removals of protein-protein interaction sites | 2.1 | 4 | Citations (PDF) |
| 45 | Experimental and computational methods for the analysis and modeling of signaling networks | 3.6 | 4 | Citations (PDF) |
| 46 | Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound | 1.9 | 5 | Citations (PDF) |
| 47 | Peamaclein – A new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3 | 1.6 | 103 | Citations (PDF) |
| 48 | Phosphoproteomic Analysis of Differentiating Leishmania Parasites Reveals a Unique Stage-Specific Phosphorylation Motif | 2.3 | 79 | Citations (PDF) |
| 49 | Exploring the diversity of SPRY/B30.2-mediated interactions | 7.4 | 78 | Citations (PDF) |
| 50 | DBATE: database of alternative transcripts expression | 1.2 | 11 | Citations (PDF) |
| 51 | webPDBinder: a server for the identification of ligand binding sites on protein structures | 11.2 | 7 | Citations (PDF) |
| 52 | Role of CTCF Protein in Regulating FMR1 Locus Transcription | 2.2 | 44 | Citations (PDF) |
| 53 | Nucleos: a web server for the identification of nucleotide-binding sites in protein structures | 11.2 | 7 | Citations (PDF) |
| 54 | Deciphering a global network of functionally associated post‐translational modifications | 3.7 | 235 | Citations (PDF) |
| 55 | Mapping the human phosphatome on growth pathways | 3.7 | 28 | Citations (PDF) |
| 56 | Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities | 2.5 | 17 | Citations (PDF) |
| 57 | Modeling gene regulatory network motifs using statecharts | 2.5 | 9 | Citations (PDF) |
| 58 | Identification of Nucleotide-Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity | 1.5 | 6 | Citations (PDF) |
| 59 | From sequence to structural analysis in protein phosphorylation motifs | 5.8 | 20 | Citations (PDF) |
| 60 | PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae | 2.1 | 19 | Citations (PDF) |
| 61 | Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani | 1.9 | 7 | Citations (PDF) |
| 62 | Phosfinder: a web server for the identification of phosphate-binding sites on protein structures | 11.2 | 14 | Citations (PDF) |
| 63 | Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites | 11.2 | 46 | Citations (PDF) |
| 64 | Phosphate binding sites identification in protein structures | 11.2 | 20 | Citations (PDF) |
| 65 | Identification of
Leishmania‐
specific protein phosphorylation sites by LC‐ESI‐MS/MS and comparative genomics analyses | 2.5 | 37 | Citations (PDF) |
| 66 | Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations | 1.5 | 14 | Citations (PDF) |
| 67 | ELM: the status of the 2010 eukaryotic linear motif resource | 11.2 | 224 | Citations (PDF) |
| 68 | Cyclosporin A Treatment of Leishmania donovani Reveals Stage-Specific Functions of Cyclophilins in Parasite Proliferation and Viability | 1.9 | 41 | Citations (PDF) |
| 69 | Modular architecture of nucleotide-binding pockets | 11.2 | 28 | Citations (PDF) |
| 70 | FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures | 2.5 | 31 | Citations (PDF) |
| 71 | Structure-based function prediction: approaches and applications | 3.9 | 75 | Citations (PDF) |
| 72 | Phospho3D: a database of three-dimensional structures of protein phosphorylation sites | 11.2 | 45 | Citations (PDF) |
| 73 | 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures | 11.2 | 6 | Citations (PDF) |
| 74 | SH3-Hunter: discovery of SH3 domain interaction sites in proteins | 11.2 | 35 | Citations (PDF) |
| 75 | Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon | 3.0 | 131 | Citations (PDF) |
| 76 | False occurrences of functional motifs in protein sequences highlight evolutionary constraints | 2.5 | 8 | Citations (PDF) |
| 77 | Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites | 2.5 | 19 | Citations (PDF) |
| 78 | A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity | 3.2 | 25 | Citations (PDF) |
| 79 | A neural strategy for the inference of SH3 domain-peptide interaction specificity | 2.5 | 10 | Citations (PDF) |
| 80 | Query3d: a new method for high-throughput analysis of functional residues in protein structures | 2.5 | 47 | Citations (PDF) |
| 81 | Seq2Struct: a resource for establishing sequence-structure links | 3.2 | 10 | Citations (PDF) |
| 82 | pdbFun: mass selection and fast comparison of annotated PDB residues | 11.2 | 31 | Citations (PDF) |
| 83 | SURFACE: a database of protein surface regions for functional annotation | 11.2 | 60 | Citations (PDF) |
| 84 | iSPOT: a web tool to infer the interaction specificity of families of protein modules | 11.2 | 30 | Citations (PDF) |
| 85 | ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins | 11.2 | 571 | Citations (PDF) |
| 86 | Searching the
MINT
Database for Protein Interaction Information | 3.2 | 0 | Citations (PDF) |
| 87 | The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation | 3.0 | 22 | Citations (PDF) |
| 88 | MINT: a Molecular INTeraction database | 1.8 | 695 | Citations (PDF) |
| 89 | Distinct Binding Specificity of the Multiple PDZ Domains of INADL, a Human Protein with Homology to INAD from Drosophila melanogaster | 1.3 | 60 | Citations (PDF) |
| 90 | Protein surface similarities: a survey of methods to describe and compare protein surfaces | 3.5 | 54 | Citations (PDF) |
| 91 | Identification of a Putative Binding Site for Negatively Charged Surfaces in the Fibronectin Type II Domain of Human Factor XII | 2.3 | 45 | Citations (PDF) |
| 92 | SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family | 3.0 | 88 | Citations (PDF) |
| 93 | Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution 1 1Edited by J. Thornton | 3.0 | 78 | Citations (PDF) |
| 94 | Design and properties of a Myc derivative that efficiently homodimerizes | 5.2 | 211 | Citations (PDF) |
| 95 | Three-dimensional profiles: a new tool to identify protein surface similarities | 3.0 | 50 | Citations (PDF) |
| 96 | Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition | 2.2 | 12 | Citations (PDF) |
| 97 | Homology modeling of Neurospora crassa geranylgeranyl pyrophosphate synthase: structural interpretation of mutant phenotypes | 2.2 | 14 | Citations (PDF) |
| 98 | Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht | 3.0 | 511 | Citations (PDF) |
| 99 | Modelling antibody-antigen interactions: ferritin as a case study | 2.0 | 17 | Citations (PDF) |
| 100 | PUZZLE: A New Method for Automated Protein Docking Based on Surface Shape Complementarity | 3.0 | 92 | Citations (PDF) |
| 101 | Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages | 3.0 | 234 | Citations (PDF) |
| 102 | Transcriptome profiling of human dermal MDPL fibroblasts reveals a characteristic molecular signature providing insights into pathogenic mechanisms | 2.8 | 0 | Citations (PDF) |
| 103 | Structural and functional impact of the POLD1 Ser605del variant in MDPL syndrome: insights from protein–protein interactions | 2.3 | 0 | Citations (PDF) |
| 104 | Gallic Acid‐Responsive
microRNAs
Reprogram Lignification During Drought Acclimation Process in Spearmint | 6.5 | 0 | Citations (PDF) |
| 105 | High-throughput sequencing reveals that microRNA-based regulation, cell wall remodeling and phytohormone signaling orchestrate wheat seminal root development | 2.6 | 0 | Citations (PDF) |
| 106 | Uncovering a Conserved miRNA Hallmark Across Diverse SARS-CoV-2-Infected Cellular Models | 0.6 | 0 | Citations (PDF) |
