List of works - Anna Panchenko

A comparison of position-specific score matrices based on sequence and structure alignments

scientific article

A structure-based method for protein sequence alignment

scientific article

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

scientific article published on 01 March 2019

Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers

scientific article

Analysis of protein homology by assessing the (dis)similarity in protein loop regions

scientific article

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols

scientific article published on January 2017

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation

scientific article published on 16 December 2015

Cancer missense mutations alter binding properties of proteins and their interaction networks

scientific article (publication date: 2013)

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

scientific article

Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer

scientific article published on 01 April 2020

Coevolution in defining the functional specificity

scientific article

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

scientific article

Comparison of sequence and structure alignments for protein domains.

scientific article

Computational Approaches to Prioritize Cancer Driver Missense Mutations

scientific article published on 20 July 2018

Computational large-scale mapping of protein-protein interactions using structural complexes

scientific article published on 24 September 2013

Correlated evolution of interacting proteins: looking behind the mirrortree

scientific article published on 09 October 2008

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

scientific article published on 14 December 2015

Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

scientific article

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

scientific article

DNA polymerase η mutational signatures are found in a variety of different types of cancer

scientific article published on 15 November 2017

Data sets on human histone interaction networks

scientific article published on 21 November 2020

Database resources of the National Center for Biotechnology Information

scientific article (published 2012-01-01)

Database resources of the National Center for Biotechnology Information

scientific article

Database resources of the National Center for Biotechnology Information

scientific article (published 2010-01-01)

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

scientific article (publication date: 2007)

Deciphering protein-protein interactions. Part I. Experimental techniques and databases

scientific article

Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms

scientific article published on 16 November 2020

Editorial overview: Dynamic protein interactions - from complexes to molecular machines

scientific article published on 01 June 2019

Editorial overview: Linking protein sequence and structural changes to function in the era of next-generation sequencing

scientific article published on 01 June 2015

Ensemble approach to predict specificity determinants: benchmarking and validation

scientific article

Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures

scientific article published on 3 December 2010

Evolution of protein binding modes in homooligomers

scientific article

Evolutionary plasticity of protein families: coupling between sequence and structure variation

scientific article published in November 2005

Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization

scientific article

Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.

scientific article published on January 2017

Exploring background mutational processes to decipher cancer genetic heterogeneity.

scientific article published on 4 May 2017

Exploring functional roles of multibinding protein interfaces

scientific article

Finding biologically relevant protein domain interactions: conserved binding mode analysis

scientific article published on 29 December 2005

Finding driver mutations in cancer: Elucidating the role of background mutational processes

scientific article published on 29 April 2019

Finding weak similarities between proteins by sequence profile comparison

scientific article

Functional specificity lies within the properties and evolutionary changes of amino acids

scientific article

Functional states of homooligomers: insights from the evolution of glycosyltransferases

scientific article

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

scientific article

Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling

scientific article published on 01 July 2019

Histone tails as signaling antennas of chromatin

scientific article published on 03 December 2020

HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants

scientific article

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites ⬇️

scientific article published on January 31, 2012

Human histone interaction networks: an old concept, new trends

scientific article published on 21 October 2020

Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

scientific article published in September 2017

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

scientific article

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites

scientific article

Intrinsic disorder and protein multibinding in domain, terminal, and linker regions

scientific article

Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis

scientific article

Intrinsic protein disorder in human pathways ⬇️

scientific article published on October 20, 2011

Knowledge-based annotation of small molecule binding sites in proteins

scientific article published in July 2010

Large‐scale mapping of human protein interactome using structural complexes ⬇️

scientific article published on March 1, 2012

Long-term trends in evolution of indels in protein sequences

scientific article

MMDB: 3D structures and macromolecular interactions

scientific article

MMDB: Entrez's 3D-structure database

scientific article

MMDB: Entrez's 3D-structure database.

scientific article

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

scientific article

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

scientific article

Modeling effects of human single nucleotide polymorphisms on protein-protein interactions

scientific article

Modeling the evolution of protein domain architectures using maximum parsimony

scientific article

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots ⬇️

scientific article published on December 16, 2011

Molecular Biology and Evolution of Cancer: From Discovery to Action

scientific article published on 01 February 2020

Molecular mechanisms of disease-causing missense mutations

scientific article

Molecular recognition of nucleosomes by binding partners

scientific article published on 13 April 2019

MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions

scientific article published on 05 May 2016

MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions

scientific article published on 27 February 2020

Mutational signatures and mutable motifs in cancer genomes.

scientific article

Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.

scientific article

Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers

scientific article

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases ⬇️

scientific article published on July 16, 2012

Phosphorylation in protein-protein binding: effect on stability and function.

scientific article

Physicochemical mechanisms of protein regulation by phosphorylation

scientific article

Physics approaches to protein interactions and gene regulation

scientific article published on 13 May 2011

Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity.

scientific article

Prediction of functional sites by analysis of sequence and structure conservation

scientific article published on 9 March 2004

Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

scientific article

Refining multiple sequence alignments with conserved core regions

scientific article

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes

scientific article

SPEER-SERVER: a web server for prediction of protein specificity determining sites ⬇️

scientific article published on June 11, 2012

State of the art: refinement of multiple sequence alignments

scientific article

State of the art: refinement of multiple sequence alignments

Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.

scientific article

Structural and functional roles of coevolved sites in proteins

scientific article

Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Structural similarity of loops in protein families: toward the understanding of protein evolution

scientific article

The foldon universe: a survey of structural similarity and self-recognition of independently folding units 1 1Edited by F. E. Cohen

The relationship of protein conservation and sequence length

scientific article

Threading with explicit models for evolutionary conservation of structure and sequence

scholarly article by Anna Panchenko published in January 1999

Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

scientific article published on 6 May 2016

[Anorexia nervosa is frequently associated with psychiatric co-morbidity] ⬇️

scientific article published on 01 September 2015

List of works by Anna Panchenko

A comparison of position-specific score matrices based on sequence and structure alignments

A structure-based method for protein sequence alignment

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers

Analysis of protein homology by assessing the (dis)similarity in protein loop regions

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation

Cancer missense mutations alter binding properties of proteins and their interaction networks

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer

Coevolution in defining the functional specificity

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

Comparison of sequence and structure alignments for protein domains.

Computational Approaches to Prioritize Cancer Driver Missense Mutations

Computational large-scale mapping of protein-protein interactions using structural complexes

Correlated evolution of interacting proteins: looking behind the mirrortree

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

DNA polymerase η mutational signatures are found in a variety of different types of cancer

Data sets on human histone interaction networks

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

Deciphering protein-protein interactions. Part I. Experimental techniques and databases

Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms

Editorial overview: Dynamic protein interactions - from complexes to molecular machines

Editorial overview: Linking protein sequence and structural changes to function in the era of next-generation sequencing

Ensemble approach to predict specificity determinants: benchmarking and validation

Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures

Evolution of protein binding modes in homooligomers

Evolutionary plasticity of protein families: coupling between sequence and structure variation

Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization

Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.

Exploring background mutational processes to decipher cancer genetic heterogeneity.

Exploring functional roles of multibinding protein interfaces

Finding biologically relevant protein domain interactions: conserved binding mode analysis

Finding driver mutations in cancer: Elucidating the role of background mutational processes

Finding weak similarities between proteins by sequence profile comparison

Functional specificity lies within the properties and evolutionary changes of amino acids

Functional states of homooligomers: insights from the evolution of glycosyltransferases

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling

Histone tails as signaling antennas of chromatin

HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites ⬇️

Human histone interaction networks: an old concept, new trends

Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites

Intrinsic disorder and protein multibinding in domain, terminal, and linker regions

Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis

Intrinsic protein disorder in human pathways ⬇️

Knowledge-based annotation of small molecule binding sites in proteins

Large‐scale mapping of human protein interactome using structural complexes ⬇️

Long-term trends in evolution of indels in protein sequences

MMDB: 3D structures and macromolecular interactions

MMDB: Entrez's 3D-structure database

MMDB: Entrez's 3D-structure database.

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

Modeling effects of human single nucleotide polymorphisms on protein-protein interactions

Modeling the evolution of protein domain architectures using maximum parsimony

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots ⬇️

Molecular Biology and Evolution of Cancer: From Discovery to Action

Molecular mechanisms of disease-causing missense mutations

Molecular recognition of nucleosomes by binding partners

MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions

MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions

Mutational signatures and mutable motifs in cancer genomes.

Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.

Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases ⬇️

Phosphorylation in protein-protein binding: effect on stability and function.

Physicochemical mechanisms of protein regulation by phosphorylation

Physics approaches to protein interactions and gene regulation

Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity.

Prediction of functional sites by analysis of sequence and structure conservation