List of works - Haim Wolfson

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core

scientific article

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

scientific article published in April 1993

A hierarchical protein folding scheme based on the building block folding model.

scientific article

A method for simultaneous alignment of multiple protein structures

scientific article

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

scientific article

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.

scientific article

ARTS: alignment of RNA tertiary structures

scientific article published on 01 September 2005

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

scientific article

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

scientific article

An integrated suite of fast docking algorithms

scientific article

Analysis and classification of RNA tertiary structures

scientific article published on 29 September 2008

Approaching the CAPRI challenge with an efficient geometry-based docking

scientific article

Automatic prediction of protein interactions with large scale motion

scientific article

Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques

scientific article

BioInfo3D: a suite of tools for structural bioinformatics

scientific article published on July 2004

Blind prediction of interfacial water positions in CAPRI

scientific article

Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer

scientific article published on 6 April 2007

Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies

scientific article

Computational validation of protein nanotubes

scientific article published on March 2009

Computer-based identification of a novel LIMK1/2 inhibitor that synergizes with salirasib to destabilize the actin cytoskeleton

scientific article

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids

scientific article

Conformational transitions in human translin enable nucleic acid binding.

scientific article published on 26 August 2013

Conservation and amyloid formation: a study of the gelsolin-like family

scientific article published in May 2003

Conservation of polar residues as hot spots at protein interfaces

scholarly article by Zengjian Hu published in June 2000

Constructing templates for protein structure prediction by simulation of protein folding pathways.

scientific article

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

scientific article

De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs

scientific article

Design of Disruptors of the Hsp90-Cdc37 Interface

scientific article published on 15 January 2020

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map ⬇️

scientific article published on November 15, 2010

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

scientific article published on September 2008

Diameter-selective dispersion of carbon nanotubes by β-lactoglobulin whey protein

scientific article published on 16 July 2013

DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes

scientific article published on 25 April 2015

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

scientific article published on 13 December 2006

EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps

scientific article

Examination of shape complementarity in docking ofUnbound proteins

article by Raquel Norel et al published 15 August 1999 in Proteins

FiberDock: Flexible induced-fit backbone refinement in molecular docking

scientific article

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

scientific article

Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis

scientific article

FireDock: a web server for fast interaction refinement in molecular docking

scientific article published on 19 April 2008

FireDock: fast interaction refinement in molecular docking

scientific article

FlexProt: alignment of flexible protein structures without a predefinition of hinge regions

scientific article

Flexible protein alignment and hinge detection

scientific article

From structure to function: methods and applications

scientific article

Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

scientific article

Geometry-based flexible and symmetric protein docking

scientific article

Hierarchical protein folding pathways: a computational study of protein fragments.

scientific article

HingeProt: automated prediction of hinges in protein structures

scientific article

How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?

scientific article

Identification of the N-terminal peptide binding site of glucose-regulated protein 94.

scientific article

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly

scientific article published on 20 February 2009

Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment

scientific article published on 01 March 2006

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit

scientific article

Memdock: an α-helical membrane protein docking algorithm

scientific article published on 8 April 2016

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation

scientific article published on 19 September 2007

Modeling of Multimolecular Complexes

scientific article published on 01 January 2020

MolAxis: a server for identification of channels in macromolecules

scientific article published on 29 April 2008

MolAxis: efficient and accurate identification of channels in macromolecules

scientific article published on October 2008

Molecular surface representations by sparse critical points

scientific article (publication date: 1994)

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

scientific article

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

scientific article

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

scientific article

Multiple structural alignment by secondary structures: algorithm and applications

scientific article published on November 2003

Novel LIMK2 Inhibitor Blocks Panc-1 Tumor Growth in a mouse xenograft model

scientific article

Novel approach for efficient pharmacophore-based virtual screening: method and applications

scientific article published on October 2009

On type of metric spaces

scientific article published in 1986

Optimization of multiple-sequence alignment based on multiple-structure alignment

scientific article

ParaDock: a flexible non-specific DNA--rigid protein docking algorithm

scientific article published on 10 August 2011

PatchDock and SymmDock: servers for rigid and symmetric docking

scientific article

PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

scientific article

PharmaGist: a webserver for ligand-based pharmacophore detection

scientific article published on 19 April 2008

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm

scientific article published on 11 March 2016

Potential folding-function interrelationship in proteins

scientific article

Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

scientific article published on January 2004

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

scientific article published on January 2004

Prediction of interacting single-stranded RNA bases by protein-binding patterns

scientific article

Prediction of multimolecular assemblies by multiple docking

scientific article

Principles of docking: An overview of search algorithms and a guide to scoring functions

scientific article (publication date: June 2002)

Principles of docking: An overview of search algorithms and a guide to scoring functions

scholarly article by Inbal Halperin published in May 2002

Principles of flexible protein-protein docking

scientific article published on November 2008

Principles of nanostructure design with protein building blocks

scientific article

Protein structure fitting and refinement guided by cryo-EM density

scientific article

Protein structure prediction using a docking-based hierarchical folding scheme

scientific article

Protein structure prediction via combinatorial assembly of sub-structural units.

scientific article

Protein-Peptide Interaction Design: PepCrawler and PinaColada

scientific article

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces

scientific article

Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking

scientific article

QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding

scientific article

Recognition of functional sites in protein structures.

scientific article

Reducing the computational complexity of protein folding via fragment folding and assembly

scientific article published in June 2003

RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

scientific article

Self-assembly of fused homo-oligomers to create nanotubes

scientific article published on January 2008

Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19.

scientific article

SiteEngines: recognition and comparison of binding sites and protein-protein interfaces

scientific article

SiteLight: binding-site prediction using phage display libraries

scientific article published on July 2003

SnapDock-template-based docking by Geometric Hashing

scientific article published in July 2017

Spatial chemical conservation of hot spot interactions in protein-protein complexes

scientific article

Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4.

scientific article

Structural similarity of genetically interacting proteins

scientific article

Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding

scientific article published on 29 January 2013

SymmRef: a flexible refinement method for symmetric multimers

scientific article published on 30 June 2011

Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers

scientific article published in April 2011

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

scientific article

The ARTS web server for aligning RNA tertiary structures

scientific article

The multiple common point set problem and its application to molecule binding pattern detection

scientific article

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism

scientific article published on October 2009

Using DelPhi to compute electrostatic potentials and assess their contribution to interactions

scientific article published in August 2003

List of works by Haim Wolfson

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core

A computer vision based technique for 3-D sequence-independent structural comparison of proteins

A hierarchical protein folding scheme based on the building block folding model.

A method for simultaneous alignment of multiple protein structures

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.

ARTS: alignment of RNA tertiary structures

Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

An integrated suite of fast docking algorithms

Analysis and classification of RNA tertiary structures

Approaching the CAPRI challenge with an efficient geometry-based docking

Automatic prediction of protein interactions with large scale motion

Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques

BioInfo3D: a suite of tools for structural bioinformatics

Blind prediction of interfacial water positions in CAPRI

Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer

Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies

Computational validation of protein nanotubes

Computer-based identification of a novel LIMK1/2 inhibitor that synergizes with salirasib to destabilize the actin cytoskeleton

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids

Conformational transitions in human translin enable nucleic acid binding.

Conservation and amyloid formation: a study of the gelsolin-like family

Conservation of polar residues as hot spots at protein interfaces

Constructing templates for protein structure prediction by simulation of protein folding pathways.

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs

Design of Disruptors of the Hsp90-Cdc37 Interface

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map ⬇️

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

Diameter-selective dispersion of carbon nanotubes by β-lactoglobulin whey protein

DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps

Examination of shape complementarity in docking ofUnbound proteins

FiberDock: Flexible induced-fit backbone refinement in molecular docking

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis

FireDock: a web server for fast interaction refinement in molecular docking

FireDock: fast interaction refinement in molecular docking

FlexProt: alignment of flexible protein structures without a predefinition of hinge regions

Flexible protein alignment and hinge detection

From structure to function: methods and applications

Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

Geometry-based flexible and symmetric protein docking

Hierarchical protein folding pathways: a computational study of protein fragments.

HingeProt: automated prediction of hinges in protein structures

How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?

Identification of the N-terminal peptide binding site of glucose-regulated protein 94.

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly

Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit

Memdock: an α-helical membrane protein docking algorithm

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation

Modeling of Multimolecular Complexes

MolAxis: a server for identification of channels in macromolecules

MolAxis: efficient and accurate identification of channels in macromolecules

Molecular surface representations by sparse critical points

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

Multiple structural alignment by secondary structures: algorithm and applications

Novel LIMK2 Inhibitor Blocks Panc-1 Tumor Growth in a mouse xenograft model

Novel approach for efficient pharmacophore-based virtual screening: method and applications

On type of metric spaces

Optimization of multiple-sequence alignment based on multiple-structure alignment

ParaDock: a flexible non-specific DNA--rigid protein docking algorithm

PatchDock and SymmDock: servers for rigid and symmetric docking

PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

PharmaGist: a webserver for ligand-based pharmacophore detection

PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm

Potential folding-function interrelationship in proteins

Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

Prediction of interacting single-stranded RNA bases by protein-binding patterns

Prediction of multimolecular assemblies by multiple docking

Principles of docking: An overview of search algorithms and a guide to scoring functions

Principles of docking: An overview of search algorithms and a guide to scoring functions

Principles of flexible protein-protein docking