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List of works by Rafael J. Najmanovich

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

scientific article

A method for localizing ligand binding pockets in protein structures

scientific article

A three-way inter-molecular network accounts for the CaVα2δ1-induced functional modulation of the pore-forming CaV1.2 subunit.

scientific article published on 27 March 2018

Achievements and challenges in structural bioinformatics and computational biophysics

scientific article

Analysis of subpocket selectivity and identification of potent selective inhibitors for matriptase and matriptase-2

scientific article published on 21 November 2014

Applications of Normal Mode Analysis Methods in Computational Protein Design

scientific article published in January 2017

Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design.

scientific article published in January 2018

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

scientific article published in February 2000

Design and synthesis of potent, selective inhibitors of matriptase.

scientific article

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

scientific article

Detection of Binding Site Molecular Interaction Field Similarities

scientific article published on 17 July 2015

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

scientific article published on 16 April 2015

Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication

scientific article published in February 2024

FlexAID

Molecular docking software

FlexAID: Revisiting Docking on Non-Native-Complex Structures

scientific article published on 24 June 2015

FlexAID: Revisiting docking on non native-complex structures

Identification of an alternative translation initiation site in the sequence of the commonly used Glutathione S-Transferase tag

scientific article published on 06 September 2018

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.

scientific article

IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

scientific article published on 30 April 2013

IsoMIF Finder: online detection of binding site molecular interaction field similarities

scientific article published on 25 October 2015

Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree

scientific article published on 8 August 2013

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

scientific article

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

scientific article published on 05 August 2021

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

scientific article published on 6 August 2015

Prediction of protein function from structure: insights from methods for the detection of local structural similarities

scientific article

Protein side-chain rearrangement in regions of point mutations

scientific article

Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes.

scientific article

Side-chain flexibility in proteins upon ligand binding.

scientific article published in May 2000

Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding

scientific article

StAR-related lipid transfer domain protein 5 binds primary bile acids

scientific article

Structural analysis of metal sites in proteins: non-heme iron sites as a case study

scientific article published on 2 March 2009

Structural and chemical profiling of the human cytosolic sulfotransferases

scientific article

Structural chemistry of the histone methyltransferases cofactor binding site.

scientific article published on 03 March 2011

Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture

scientific article published in January 2008

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

scientific article

The DynaSig-ML Python package: automated learning of biomolecular dynamics–function relationships

scientific article published in 2023

The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes

scientific article published in 2021

The collapse transition in the HP model

The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

scientific article

Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages

scientific article published in September 2009

Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages

Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

scientific article published on 5 November 2014

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