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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

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Showing 1-25 of 45 citing articles:

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations
Gennady M. Verkhivker, Steve Agajanian, Deniz Yazar Oztas, et al.
Biochemistry (2021) Vol. 60, Iss. 19, pp. 1459-1484
Open Access | Times Cited: 77
Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches
Gennady M. Verkhivker, Luisa Di Paola
The Journal of Physical Chemistry B (2021) Vol. 125, Iss. 3, pp. 850-873
Closed Access | Times Cited: 73
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies
Gennady M. Verkhivker, Luisa Di Paola
The Journal of Physical Chemistry B (2021) Vol. 125, Iss. 18, pp. 4596-4619
Closed Access | Times Cited: 72
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms
Sian Xiao, Mohammed Alshahrani, Grace Gupta, et al.
Journal of Chemical Information and Modeling (2023) Vol. 63, Iss. 16, pp. 5272-5296
Open Access | Times Cited: 28
Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes
Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
Viruses (2023) Vol. 15, Iss. 5, pp. 1143-1143
Open Access | Times Cited: 22
Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots
Gennady M. Verkhivker, Steve Agajanian, Deniz Yaşar Öztaş, et al.
Journal of Chemical Theory and Computation (2021) Vol. 17, Iss. 7, pp. 4578-4598
Closed Access | Times Cited: 52
Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships
Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, et al.
Physical Chemistry Chemical Physics (2023) Vol. 25, Iss. 32, pp. 21245-21266
Open Access | Times Cited: 12
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling
Gennady M. Verkhivker, Steve Agajanian, Deniz Yaşar Öztaş, et al.
Journal of Chemical Information and Modeling (2021) Vol. 61, Iss. 10, pp. 5172-5191
Open Access | Times Cited: 29
Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets
Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, et al.
International Journal of Molecular Sciences (2022) Vol. 23, Iss. 19, pp. 11542-11542
Open Access | Times Cited: 20
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations
Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, et al.
International Journal of Molecular Sciences (2022) Vol. 23, Iss. 8, pp. 4376-4376
Open Access | Times Cited: 17
Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering
Gennady M. Verkhivker
International Journal of Molecular Sciences (2022) Vol. 23, Iss. 6, pp. 2928-2928
Open Access | Times Cited: 16
Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica
José Arturo Molina-Mora
Gene Reports (2022) Vol. 27, pp. 101554-101554
Open Access | Times Cited: 14
Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant
Gennady M. Verkhivker
International Journal of Molecular Sciences (2022) Vol. 23, Iss. 4, pp. 2172-2172
Open Access | Times Cited: 10
Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages : Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes
Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 5
Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants
Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
International Journal of Molecular Sciences (2023) Vol. 24, Iss. 7, pp. 6642-6642
Open Access | Times Cited: 5
Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation
Gennady M. Verkhivker, Steve Agajanian, Deniz Yaşar Öztaş, et al.
Journal of Biomolecular Structure and Dynamics (2021) Vol. 40, Iss. 20, pp. 9724-9741
Open Access | Times Cited: 13
Computational Analysis of Protein Stability and Allosteric Interaction Networks in Distinct Conformational Forms of the SARS-CoV-2 Spike D614G Mutant: Reconciling Functional Mechanisms through Allosteric Model of Spike Regulation
Gennady M. Verkhivker, Steve Agajanian, Denis Oztas, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2021)
Closed Access | Times Cited: 11
Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant
Gennady M. Verkhivker, Steve Agajanian, Deniz Yaşar Öztaş, et al.
ACS Omega (2021) Vol. 6, Iss. 24, pp. 16216-16233
Open Access | Times Cited: 11
Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms
Gennady M. Verkhivker, Steve Agajanian, Deniz Yaşar Öztaş, et al.
ACS Omega (2021) Vol. 6, Iss. 40, pp. 26354-26371
Open Access | Times Cited: 11
Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity
Kanchanok Kodchakorn, Prachya Kongtawelert
PLoS ONE (2022) Vol. 17, Iss. 11, pp. e0277745-e0277745
Open Access | Times Cited: 7
Mutational scanning of spike RBD protein for enhanced ACE2 affinity emerging Southeast Asia in the late transmission phase
Kanchanok Kodchakorn, Tawan Chokepaichitkool, Prachya Kongtawelert
Scientific Reports (2022) Vol. 12, Iss. 1
Open Access | Times Cited: 5
Probing structural basis for enhanced binding of SARS‐CoV‐2 P.1 variant spike protein with the human ACE2 receptor
Surabhi Lata, M. Akif
Journal of Cellular Biochemistry (2022) Vol. 123, Iss. 7, pp. 1207-1221
Open Access | Times Cited: 5
Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness
Yanan Fu, Yanping Huang, Jingjing Rao, et al.
Archives of Virology (2022) Vol. 167, Iss. 12, pp. 2677-2688
Open Access | Times Cited: 5
Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants
Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 2
E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces
Vitor Pimentel Dos Santos, André Rodrigues, Gabriel Dutra, et al.
PeerJ (2022) Vol. 10, pp. e13099-e13099
Open Access | Times Cited: 4
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