List of works - Alessandro Pandini

Artificial neural networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry.

scientific article published on January 2013

BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

scientific article published on 02 December 2013

Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.

scientific article published on 07 December 2016

Bridging topological and functional information in protein interaction networks by short loops profiling

scientific article

Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor

scientific article published on 12 November 2015

Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

scientific article published on 14 January 2013

Computational approaches to shed light on molecular mechanisms in biological processes

scientific article

Conformational and functional analysis of molecular dynamics trajectories by self-organising maps

scientific article published on 14 May 2011

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

scientific article published on 31 May 2019

Conservation and specialization in PAS domain dynamics.

scientific article published in March 2005

Detecting similarities among distant homologous proteins by comparison of domain flexibilities.

scientific article published on 15 June 2007

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

scientific article published on 9 November 2011

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.

scientific article

Dynamic Profiling of β-Coronavirus 3CL M<sup>pro</sup> Protease Ligand-Binding Sites

scientific article published on 14 June 2021

Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.

scientific article published in October 2012

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

scientific article published on 05 June 2013

In silico identification of rescue sites by double force scanning

scientific article published on 14 August 2017

Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

scientific article published on 28 February 2018

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

publication published on 12 April 2021

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database

scientific article published on 3 January 2007

PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations

scientific article published on 25 February 2022

Predicting the accuracy of protein-ligand docking on homology models.

scientific article

PyCoM: a python library for large-scale analysis of residue–residue coevolution data

scientific article published in 2024

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

scientific article published on 27 September 2013

Structural alphabets derived from attractors in conformational space.

scientific article

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis

scientific article

The Gearbox of the Bacterial Flagellar Motor Switch.

scientific article published on 23 June 2016

The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

scientific article

The crystal structure of the human titin:obscurin complex reveals a conserved yet specific muscle M-band zipper module

scientific article

Using Local States To Drive the Sampling of Global Conformations in Proteins

scientific article published on 25 January 2016

List of works by Alessandro Pandini

Artificial neural networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry.

BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.

Bridging topological and functional information in protein interaction networks by short loops profiling

Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor

Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

Computational approaches to shed light on molecular mechanisms in biological processes

Conformational and functional analysis of molecular dynamics trajectories by self-organising maps

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

Conservation and specialization in PAS domain dynamics.

Detecting similarities among distant homologous proteins by comparison of domain flexibilities.

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.

Dynamic Profiling of β-Coronavirus 3CL M<sup>pro</sup> Protease Ligand-Binding Sites

Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

In silico identification of rescue sites by double force scanning

Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database

PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations

Predicting the accuracy of protein-ligand docking on homology models.

PyCoM: a python library for large-scale analysis of residue–residue coevolution data

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

Structural alphabets derived from attractors in conformational space.

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis

The Gearbox of the Bacterial Flagellar Motor Switch.

The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

The crystal structure of the human titin:obscurin complex reveals a conserved yet specific muscle M-band zipper module

Using Local States To Drive the Sampling of Global Conformations in Proteins