List of works - Alberto Perez

8-Amino guanine accelerates tetramolecular G-quadruplex formation.

scientific article

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

scientific article

Accelerating molecular simulations of proteins using Bayesian inference on weak information.

scientific article

Accelerating physical simulations of proteins by leveraging external knowledge.

scientific article

Advances in free-energy-based simulations of protein folding and ligand binding.

scientific article

Assessment of protein structure refinement in CASP9.

scientific article

Binding Ensembles of <i>p53</i>-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

scientific article published on 02 January 2021

Blind protein structure prediction using accelerated free-energy simulations

scientific article

Computing the relative stabilities and the per-residue components in protein conformational changes.

scientific article

Constraint methods that accelerate free-energy simulations of biomolecules

scientific article

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

scientific article published on 04 February 2021

DNAlive: a tool for the physical analysis of DNA at the genomic scale

scientific article

Determining promoter location based on DNA structure first-principles calculations

scientific article

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

scientific article

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management

scientific article published on 14 February 2006

Exploring early stages of the chemical unfolding of proteins at the proteome scale

scientific article (publication date: 2013)

Exploring polymorphisms in B-DNA helical conformations.

scientific article published on 24 September 2012

Exploring the Essential Dynamics of B-DNA

scientific article published on 01 September 2005

Extracting representative structures from protein conformational ensembles.

scientific article published on 5 July 2014

Frontiers in Molecular Dynamics Simulations of DNA ⬇️

scientific article published on August 10, 2011

Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations

scientific article published on 17 September 2015

High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid-State NMR Restraints

scientific article published on 17 April 2019

Impact of methylation on the physical properties of DNA.

scientific article published on May 2012

MELD x MD Folds Nonthreadables, Giving Native Structures and Populations

scientific article published on 21 November 2018

MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths

scientific article

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge

scientific article published on 12 November 2018

NMR-assisted protein structure prediction with MELDxMD

scientific article published on 08 August 2019

Parmbsc1: a refined force field for DNA simulations ⬇️

scientific article

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

scientific article

Real-time atomistic description of DNA unfolding

scientific article published on 01 June 2010

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.

scientific article published on August 2015

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

scientific article (publication date: June 2007)

Regulation of the activity of the promoter of RNA-induced silencing, C3PO.

scientific article published on 16 July 2017

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

scientific article published in October 2004

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

scientific article

The lipid raft proteome of Borrelia burgdorferi

scientific article published on 10 August 2015

Theoretical methods for the simulation of nucleic acids.

scientific article published on November 2003

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

scientific article

List of works by Alberto Perez

8-Amino guanine accelerates tetramolecular G-quadruplex formation.

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Accelerating molecular simulations of proteins using Bayesian inference on weak information.

Accelerating physical simulations of proteins by leveraging external knowledge.

Advances in free-energy-based simulations of protein folding and ligand binding.

Assessment of protein structure refinement in CASP9.

Binding Ensembles of <i>p53</i>-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Blind protein structure prediction using accelerated free-energy simulations

Computing the relative stabilities and the per-residue components in protein conformational changes.

Constraint methods that accelerate free-energy simulations of biomolecules

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

DNAlive: a tool for the physical analysis of DNA at the genomic scale

Determining promoter location based on DNA structure first-principles calculations

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management

Exploring early stages of the chemical unfolding of proteins at the proteome scale

Exploring polymorphisms in B-DNA helical conformations.

Exploring the Essential Dynamics of B-DNA

Extracting representative structures from protein conformational ensembles.

Frontiers in Molecular Dynamics Simulations of DNA ⬇️

Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations

High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid-State NMR Restraints

Impact of methylation on the physical properties of DNA.

MELD x MD Folds Nonthreadables, Giving Native Structures and Populations

MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge

NMR-assisted protein structure prediction with MELDxMD

Parmbsc1: a refined force field for DNA simulations ⬇️

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Real-time atomistic description of DNA unfolding

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

Regulation of the activity of the promoter of RNA-induced silencing, C3PO.

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

The lipid raft proteome of Borrelia burgdorferi

Theoretical methods for the simulation of nucleic acids.

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA