ALLIN – Annotation of sequence aLignment and structuraL ProteIn visualizatioN
Software
ALLIN - (Annotation of sequence aLignment and structuraL ProteIn visualizatioN) is a web interface to generate an interactive HTML web page for the simultaneously visualization of annotated protein sequences alignment and 3D structures or homology models of the related proteins. The physiological, functional, and structural properties of proteins and their pathogenic variants can be summarized using many tools. The amount of information relating to a single protein is large, often spread among different sources that require different programs to access. It is not always easy to select, simultaneously visualize, and compare specific properties of different proteins. On the other hand,...
ALPACA
Software
This software allows you to use machine learning based classifiers of cannabinoid receptor subtype 1 (CB1R) affinity, cannabinoid receptor subtype 2 (CB2R) affinity and CB2R/CB1R selectivity. ALPACA does not require any specific cheminformatics or programming skill and offers the capability to conduct virtual screening campaigns by inputting a list of SMILES strings, hence enabling the identification of highly probable CB2R selective molecules with a high level of confidence.
AMALPHI
Software
This software allows you to use an artificial intelligence model developed to predict which drug candidates may cause drug-induced phospholipidosis (PLD), a condition where phospholipids accumulate in cells due to prolonged exposure to certain types of drugs. This condition is often associated with cationic amphiphilic drugs (CAD). PLD is a significant concern in drug development and has posed challenges in antiviral research for the SARS-CoV-2 virus. The artificial intelligence model was trained on a dataset containing 545 carefully selected molecules from ChEMBL v30. The best model, created using the Balanced Random Forest algorithm, achieved excellent results, with an AUC (Area...
Bio-macromolecule purification, crystallization and characterization by structural biology X-ray techniques
Academic collaboration, Facility, Skill, Software
Our expertise lies in purification and advanced characterization by X-ray-based techniques of bio-macromolecules to perform cutting-edge structural biology investigations on proteins and their complexes. Our proven experience enables us to handle challenging systems such as membrane proteins and protein-ligand complexes. Regarding protein-ligand adducts for crystallographic studies, in addition to standard soaking experiments using single ligands, we also perform fragment screening for rational drug design. We offer the opportunity to perform structural biology studies by X-ray diffraction for high-resolution structure determination and provide established proficiency to obtain crystal structure information about protein-ligand interactions. Moreover, we are experts in Bio Small-Angle X-ray...
Bioinformatics and Computational Biology for structure-function of proteins
Academic collaboration, Skill, Software
The Laboratory has a well-established experience in the study of structure-function relationships of proteins, with particular focus on protein stability, effects of mutations, protein-ligand interaction
Bioinformatics for structural biology
Skill, Software
The Bioinformatic group in Segrate (Mi) features a computational infrastructure present at ITB-Milano, which consist of a high performance storage (about 1 PB), a high performance computer cluster (about 1200 core, 18 GPU and 3 A100). Group skills consist of: classical molecular dynamics simulations on different types of biomolecules (Protein, RNA and DNA), also for large systems, to study the effects of mutations, PTM, also for RNA, or molecules binding, metadynamics, protein – ligand and protein – protein docking, High Throughput Virtual Screening.
Computational Biology, Computational Enzymology, Drug Discovery, Molecular recognition, Protein-Protein-peptide interaction, Peptide design and synthesis, High Performance Computing, Surface Plasmon Resonance, ELISA, Antibody characterization
Academic collaboration, Facility, Research field/topic, Skill, Software
The Structural Biology Group at CNR-ICCOM focuses on exploring the relationship between the structure, dynamics, and function of biomolecules using a combination of computational biology tools, synthetic chemistry, and biomolecular recognition techniques. Computational Laboratory The group employs advanced methods such as molecular dynamics simulations, docking, drug discovery, and bioinformatics (from quantum to empirical force-fields) to investigate and design biological systems, ranging from small molecules and peptides to proteins and nucleic acids. Key research areas include: 1. Molecular Effects of Sequence-Structure Perturbations: Investigating the impact of binding events and mutations on the activity and interactions of proteins involved in critical biological...
Computational Chemistry and Cheminformatics, StOrMoDB platform, EHBAS platform
Facility, Research field/topic, Skill, Software
The main computational chemistry skills in the ICB Computational Chemistry and Cheminformatics group (ICB-CCC) cover the fields of homology modelling, molecular docking and molecular dynamics simulations of biomolecular systems and quantum chemistry calculations on isolated molecules or their complexes with representative protein fragments. These skills are mainly aimed at studying the driving forces at molecular level of ligand-protein interactions, the molecular bases of receptor selectivity, and the conformational transitions associated to the modulation of receptor activities. As for the main application areas of these techniques and approaches, ICB-CCC devotes a special attention to the characterization of nuclear receptors, GPCRs and...
Computational Chemistry, HPC Clusters, simulation software
Academic collaboration, Facility, Research field/topic, Skill, Software
Computational chemistry and molecular modeling. Both quantum chemistry calculations and classical reactive/non-reactive molecular dynamics simulation methods are employed. These are creatively used to investigate the conformational and physicochemical properties, dynamics, and reactivity of oligopeptides, proteins, enzymes, DNA/RNA/PNA, lipids, micelles, membranes, cellulose-based materials, polymers, small molecules, etc., in the gas phase, in solution (explicit molecules or a continuum medium), and contact with various types of inorganic interfaces (hybrid complexes). The structure and dynamics of metal and metal oxide nanoparticles (various morphologies and sizes) functionalized with different types of molecules are simulated with appropriately parametrized reactive force fields (ReaxFF - missing parameters...
CUBE Computational Unit for Biological Exploration
Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill, Software
Background and skills: Recent years have seen ground-breaking achievements of deep-learning methods applied to the 3D structure predictions of biomacromolecules, with the phenomenal success of AlphaFold software in obtaining protein structures at an unprecedented level of accuracy. The availability of huge data on predicted protein structures is revolutionizing the field of experimental structural biology (based on classical X-ray, NMR and Cry-EM methods) making the frontier between experimental and computational approaches more and more blurred. In this context, it is increasingly important to integrate the outcomes from the different techniques in order to favour the mutual exchange, validation, enhancement of experimental...
DeLA-Drug and DeLA-DrugSelf
Software
Deep-learning-based software tools for the generation of drug-like analogs of active compounds. DeLA-Drug and DeLA-DrugSelf offer rapid generation of focused libraries for high-throughput screening without the need for time-consuming fine-tuning procedures, making them suitable for de novo design even in low-data scenarios. Accessible via free web platforms (http://www.ba.ic.cnr.it/softwareic/deladrugportal/ and https://www.ba.ic.cnr.it/softwareic/delaself/ ), both the tools can be used by medicinal chemists seeking to generate analogs of compounds already present in their laboratories, facilitating easy and cost-effective synthesis.
In silico Drug Discovery. Instrumentation: Server ; Software: Schrodinger suite and AMBER
Academic collaboration, Facility, Skill, Software
In silico Drug Discovery: Chimico computazionale con una solida formazione in sintesi organica e un’approfondita esperienza nel supporto a programmi di ottimizzazione per la scoperta di farmaci. Competenza nello sviluppo e nell’applicazione di tecnologie di screening virtuale, inclusi modelli farmacoforici basati sulla struttura e sul ligando, nonché calcoli di docking. Esperto in 3D QSAR, modellistica per omologia, ADME-Tox e nell’implementazione di cascate di screening virtuale. Particolare interesse nel riposizionamento di farmaci utilizzando approcci in silico e nell’impiego della genetica per identificare target farmacologici innovativi. La struttura informatica dispone di una capacità di archiviazione e di prestazioni computazionali elevate, adatte a...
In silico structural biology to solve biological mechanisms and guide drug discovery
Academic collaboration, Facility, Patent, Research field/topic, Skill, Software
The Laboratory of Molecular Modeling and Virtual Screening (MMVS_Lab) at SCITEC-Rome integrates diverse computational expertise to investigate biological structures and processes: -Computational Chemistry: molecular dynamics simulations of biological molecules; quantum mechanical methods to analyze molecular properties; molecular docking to predict ligand-protein and protein-protein binding interactions. -Molecular Modeling: structural homology; fold recognition; conformational analysis. -Computer Science and Data Science: use of supercomputers/high-performance computing (HPC) facilities at European computing centers for complex simulations; application of machine learning and artificial intelligence (AI) to predict molecular structures and behaviors. -Bioinformatics: Sequence analysis for the prediction of functional domains and structural features of proteins. -Drug...
Laboratorio di Biologia Molecolare e Strutturale (BMS)
Academic collaboration, Facility, Skill, Software
SKILLS AND COLLABORATIONS The team (see above) uses a wide range of methodologies to unravel complex biology problems, including molecular biology, x-ray crystallography, biophysics, and computational work (molecular modelling and dynamics, docking). The Team actively cooperates with microbiologists, immunologists and cell biologists (e.g. Imperial college London, UCD Dublin, Munich University, Harvard University, Karlsruhe Institute of Technology) and is involved in PNRR projects PE13 INF-ACT, CN1 and CN3. INSTRUMENTATION The molecular biology Labs of this team (Labs 8 and 9) are located in Via Pietro Castellino 111, Naples, and are equipped with (non-exhaustive list) T 100 Thermal Cycler (BIO-RAD), Fume cupboard...
Light scattering, spectroscopy, microscopy, calorimetry, rheology, chromatography, cell culture devices, supercomputing and data-storage resources
Facility, Software
Spectroscopy: JASCO J-815 Circular Dichroism; SHIMADZU UV-VIS Spectrophotometer; JASCO FP6500 Spectro fluorimeter; THERMO Ascent FL Fluoroscan HAMAMATSU C9413 FCS Unit; Spectrofluorimeter CARY Agilent Eclypse, equipped with thermostated control, microplane reader and polarization module Static and Dynamic Light scattering: BROOKHAVEN SM200 Spectrometers BROOKHAVEN BI9000 Correlators BROOKHAVEN BI-DNDC Differential refractometer Homemade CCD Low angle scattering system Calorimetry: TA INSTRUMENTS Nano DSC TA INSTRUMENTS Nano ITC HART 707 Microcalorimeter Microscopy: NIKON Eclipse Ti fluorescence Microscope; JPK AFM NanoWizard 3, coupled with NIKON Eclipse Ti Optical Microscope and Temperature controlled Petri Dish Heater; NIKON Eclipse 80i fluorescence Microscope Rheology facilities: TA INSTRUMENTS AR1000 Rheometer...
Membrane protein structure/function relationships
Academic collaboration, Research field/topic, Skill, Software
Study of structure/function relationships of membrane proteins by combining in silico approahces with recombinant protein production, site directed mutagenesis and in vitro activity assay
Molecular dynamics simulations of biological systems at classical and quantum-classical (QM/MM) level. Virtual screening simulations.
Academic collaboration, Skill, Software
The Magistrato Lab research activity is devoted to the development and application of state-of-the-art computational methods for multi-scale molecular simulations. We aim to investigate the structure, function, and dynamics of complex biological systems and to the development of small-molecule inhibitor to modulate their function. Our research activity ranges from the study of pharmacologically relevant enzymes, to that of protein/RNA machineries, metal ions transporters and cytolytic toxins. Our research lies at the interface of chemistry, biology and medicinal chemistry and involves collaborations with various experimental labs We have different software to run classical MD simulations (GROMACS, AMBER, PLUMED) and QM/MM (CPMD,...
Molecular dynamics, modeling, AI-based protein design.
Research field/topic, Skill, Software
Molecular Dynamics (MD): We simulate proteins to study the physical movements of atoms and molecules over time. By applying classical or biased mechanics, MD provides insights into the dynamic behavior of molecular systems, including stability, effect of mutations, binding sites. AI-Based Protein Design: We apply cutting-edge approaches that use machine learning algorithms to create, optimize, or predict the structure of proteins.
Production and characterization of soluble and membrane proteins involved in riboflavin homeostasis and related diseases
Academic collaboration, Facility, Research field/topic, Skill, Software
The laboratory of DBBA of the University of Bari (Convenzione operativa tra IBIOM e Università di Bari, prot n. 0174808 del 24/05/2024) is equipped with a Gilson HPLC system with a FP-2020 Plus Jasco fluorescence detector and Unipoint system software; a spectrophotometer; a FP-3800 spectrofluorometer; and laboratory equipment for molecular biology. At DBBA modern laboratory rooms are organised as multidisciplinary technological core consisting of different platforms: 1) proteomics 2) genomics 3) cellular engineering and biology 4) sub-cellular biochemistry and biophysics 5) Imaging facilities. DBBA also has an animal house and rooms for culturing mammalian cells and bacteria, yeasts and invertebrates...
Proteomic and Genomic analysis, In silico protein analysis, MALDI-TOF mass spectrometry
Facility, Skill, Software
Expertise in the field of protein study by top-down and bottom-up proteomic approach using LC-MALDI-TOF mass spectrometry. Expertise in human genetic analysis mainly in the field of neurological diseases by DNA sequencing (Sanger) and qPCR. In silico protein 3D structure analysis (using Chimera X software) and Molecular Dinamic Analysis (using Gromacs software) in order to study the functional effect of our sample with human mutated proteins. Collection of viable cellular samples from patients carrying genetic mutations (not certified as a biobank).
SIGMAP
Software
This software enables the use of a machine learning-based classifier for predicting sigma-1 receptor (S1R) affinity. The model was developed using the Support Vector Machine (SVM) algorithm with Morgan fingerprints as molecular descriptors. To enhance transparency and trustworthiness, the tool incorporates Explainable Artificial Intelligence (XAI) techniques, providing users with interpretable insights into the predictions. With its intuitive interface, robust predictive capabilities, and integrated XAI features, SIGMAP offers a powerful solution for the rational design of novel S1R modulators.
Single Particle Anaysis, ElectronTomography, Cryo Electron Microscopy
Academic collaboration, Facility, Patent, Research field/topic, Skill, Software
The Cryo Electron Microscopy (Cryo-EM) laboratory at ISASI Naples (EYELAB) offers advanced facilities and expertise for identifying, visualizing, and characterizing biological macromolecules in their native states. It supports a comprehensive approach to studying the structure and function of proteins, nucleic acids, and other macromolecules, as well as their interactions within cells and tissues. The laboratory offers high-resolution structural analysis through Single Particle Analysis (SPA) and Electron Tomography (ET). SPA reveals the 3D structures of proteins, enzymes, and complexes in their hydrated states, providing unprecedented detail on their architecture and function. ET enables 3D visualization of cellular structures, and tissues, shedding...
Structural Characterization of Biologically Relevant Molecules Across Varied Complexity Levels: Method Development, Software Implementation and Applications
Research field/topic, Skill, Software
The IC-CRYST team is a multidisciplinary group internationally recognized for advancing biomolecu-lar crystallography, from small compounds to macromolecules, and developing innovative software such as SIR for single-crystal and EXPO for powder diffraction data. Collaborating with academic and industrial partners, including pharmaceutical companies, the team excels in solving complex cases, determining protein structures, and characterizing drug compounds. Their strength lies in tai-loring in-house crystallographic tools to address the unique challenges of each case. Key Competencies in Bio-Crystallography: Structural Determination of Biological Macromolecules - Ab Initio Approaches Effective phasing strategies, utilizing SIR software, for accurate ab initio structural analysis of complex biological...
Synergistic use of experimental data and computational modeling for the structural investigation of biological macromolecules
Academic collaboration, Skill, Software
We develop computational tools for the analysis of big data and apply them to improve structural knowledge about biological macromolecules. The computer program RootProf [https://www.ba.ic.cnr.it/softwareic/rootprof/] allows to analyze data collected from in situ experiments according to the Modulated Enhanced Diffraction theoretical framework [https://journals.iucr.org/paper?S1600576715017070], to fast extract main trends in data and the experimental signal from active atoms (i.e. those responding to the stimulus applied in situ to the system investigated). In addition, RootProf allows combining experimental data from different techniques collected on the same sample. The computer program T-PAD [https://www.ba.ic.cnr.it/softwareic/T-PAD/] analyzes data generated by molecular dynamics (MD) to characterize local...
Theoretical modeling of photophysical, photochemical and photobiological properties
Skill, Software
Photophysics of oligonucleotides and chromophores in proteins. Photodamage, photoprotection, photoisomerization. Computational spectroscopy, like absorption and ECD of proteins and ologonucleotides. Software for simulating electronic spectra
Vibrational spectroscopy FTIR/Raman/Raman SERS for protein analysis
Academic collaboration, Facility, Research field/topic, Skill, Software
Vibrational spectroscopy FTIR/Raman/Raman SERS for biomolecule analysis ICCOM Pisa has instrumentation and consolidated skills in the field of biomacromolecule identification in biological complex systems (tissues and cells) by FTIR, Raman and Raman-SERS (Bramanti, Legnaioli, Campanella), and conformational analysis of proteins (Bramanti), including skills for extracting information from spectroscopic data using advanced chemometric tools (Campanella). ICCOM team has also a facilities and skills for the characterization of proteins by UV spectroscopy, Fluorescence spectroscopy, and liquid chromatography and for study of surface tension and viscosity of proteins by a home made dynamic surface tension detector (DSTD). These facilities allow strict collaborations with...