Sandor Vajda

Affiliations

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.
Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States.

Publications (26)

Subnanometer cobalt oxide clusters as selective low temperature oxidative dehydrogenation catalysts.

Nature communications

Avec: Sungsik Lee , Avik Halder , Glen A Ferguson , Sönke Seifert , Randall E Winans , Detre Teschner , Robert Schlögl , Vasiliki Papaefthimiou , Jeffrey Greeley , Larry A Curtiss , Stefan Vajda

Using first principles calculations to interpret XANES experiments: extracting the size-dependence of the (p , T) phase diagram of sub-nanometer Cu clusters in an O

Journal of physics. Condensed matter : an Institute of Physics journal

Avec: Nisha Mammen , Leonardo Spanu , Eric C Tyo , Bing Yang , Avik Halder , Sönke Seifert , Michael J Pellin , Stefan Vajda , Shobhana Narasimhan

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.

Journal of chemical information and modeling

Avec: Amanda E Wakefield , Christine Yueh , Dmitri Beglov , Marcelo S Castilho , Dima Kozakov , György M Keserű , Adrian Whitty ,

Probing Active Sites in Cu

ACS applied materials & interfaces

Avec: Yang Liu , Avik Halder , Soenke Seifert , Nicholas Marcella , Stefan Vajda , Anatoly I Frenkel

Improved cluster ranking in protein-protein docking using a regression approach.

Computational and structural biotechnology journal

Avec: Shahabeddin Sotudian , Israel T Desta , Nasser Hashemi , Shahrooz Zarbafian , Dima Kozakov , Pirooz Vakili , Ioannis Ch Paschalidis

FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.

Journal of molecular biology

Avec: Megan Egbert , George Jones , Matthew R Collins , Dima Kozakov ,

Improved prediction of MHC-peptide binding using protein language models.

Frontiers in bioinformatics

Avec: Nasser Hashemi , Boran Hao , Mikhail Ignatov , Ioannis Ch Paschalidis , Pirooz Vakili , Dima Kozakov

Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server.

Proteins

Avec: Sergei Kotelnikov , Ryota Ashizawa , Konstantin I Popov , Omeir Khan , Mikhail Ignatov , Stan Xiaogang Li , Mosavverul Hassan , Evangelos A Coutsias , Gennady Poda , Dzmitry Padhorny , Alexander Tropsha , Dima Kozakov

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.

Journal of chemical information and modeling

Avec: Omeir Khan , George Jones , Maria Lazou , Diane Joseph-McCarthy , Dima Kozakov , Dmitri Beglov ,

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.

Journal of chemical information and modeling

Avec: Ayse A Bekar-Cesaretli , Omeir Khan , Thu Nguyen , Dima Kozakov , Diane Joseph-Mccarthy ,

Why Some Targets Benefit from beyond Rule of Five Drugs.

Journal of medicinal chemistry

Avec: Megan Egbert , Adrian Whitty , György M Keserű ,

Structural reversibility of Cu doped NU-1000 MOFs under hydrogenation conditions.

The Journal of chemical physics

Avec: Avik Halder , Sungsik Lee , Bing Yang , Michael J Pellin , Stefan Vajda , Zhanyong Li , Ying Yang , Omar K Farha , Joseph T Hupp

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.

Proteins

Avec: Dzmitry Padhorny , Kathryn A Porter , Mikhail Ignatov , Andrey Alekseenko , Dmitri Beglov , Sergei Kotelnikov , Ryota Ashizawa , Israel Desta , Nawsad Alam , Zhuyezi Sun , Emiliano Brini , Ken Dill , Ora Schueler-Furman , Dima Kozakov

The journal of physical chemistry. A

Avec: Avik Halder , Anh T Ngo , Xiangyi Luo , Hsien-Hau Wang , J G Wen , Pedram Abbasi , Mohammad Asadi , Chengji Zhang , Dean Miller , Dongzhou Zhang , Jun Lu , Paul C Redfern , Kah Chun Lau , Rachid Amine , Rajeev S Assary , Yun Jung Lee , Amin Salehi-Khojin , Stefan Vajda , Khalil Amine , Larry A Curtiss

Amidino-Rocaglates: A Potent Class of eIF4A Inhibitors.

Cell chemical biology

Avec: Jennifer Chu , Wenhan Zhang , Regina Cencic , William G Devine , Dmitri Beglov , Thomas Henkel , Lauren E Brown , John A Porco , Jerry Pelletier

Nanoassemblies of ultrasmall clusters with remarkable activity in carbon dioxide conversion into C1 fuels.

Nanoscale

Avec: Avik Halder , Joseph Kioseoglou , Bing Yang , Karthika Lakshmi Kolipaka , Soenke Seifert , Jan Ilavsky , Michael Pellin , Mukhles Sowwan , Panagiotis Grammatikopoulos , Stefan Vajda

Analysis of tractable allosteric sites in G protein-coupled receptors.

Scientific reports

Avec: Amanda E Wakefield , Jonathan S Mason , György M Keserű

Structure-based Druggability Assessment of Anti-virulence Targets from Pseudomonas aeruginosa.

Current protein & peptide science

Avec: Thamires Q Froes , Regina L Baldini , Marcelo S Castilho

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).

Biochemistry

Avec: Mengqi Zhong , Andrew Lynch , Samantha N Muellers , Stefan Jehle , Lingqi Luo , David R Hall , Reina Iwase , James P Carolan , Megan Egbert , Amanda Wakefield , Kristina Streu , Christine M Harvey , Paula C Ortet , Dima Kozakov , Karen N Allen , Adrian Whitty

Assessing the binding properties of CASP14 targets and models.

Proteins

Avec: Megan Egbert , Usman Ghani , Ryota Ashizawa , Sergei Kotelnikov , Thu Nguyen , Israel Desta , Nasser Hashemi , Dzmitry Padhorny , Dima Kozakov ,

Use of Solvent Mapping for Characterizing the Binding Site and for Predicting the Inhibition of the Human Ether-á-Go-Go-Related K

Chemical research in toxicology

Avec: Shifan Ma , Zhuyezi Sun , Yankang Jing , Mark McGann , Istvan J Enyedy

Mechanism of Catalytic CO

The journal of physical chemistry. C, Nanomaterials and interfaces

Avec: Antonija Mravak , Stefan Vajda , Vlasta Bonačić-Koutecký

API Development Increases Access to Shared Computing Resources at Boston University.

Journal of software engineering and applications

Avec: George Jones , Amanda E Wakefield , Jeff Triplett , Kojo Idrissa , James Goebel , Dima Kozakov ,

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

bioRxiv : the preprint server for biology

Avec: Ernest Glukhov , Dmytro Kalitin , Darya Stepanenko , Yimin Zhu , Thu Nguen , George Jones , Carlos Simmerling , Julie C Mitchell , Ken A Dill , Dzmitry Padhorny , Dima Kozakov

Which cryptic sites are feasible drug targets?

Drug discovery today

Avec: Maria Lazou , Dima Kozakov , Diane Joseph-Mccarthy ,

Structure-Based Analysis of Cryptic-Site Opening.

Structure (London, England : 1993)

Avec: Zhuyezi Sun , Amanda Elizabeth Wakefield , Istvan Kolossvary , Dmitri Beglov ,

Réseau de co-auteurs

Dima Kozakov 13 collaborations

Stefan Vajda 7 collaborations

Avik Halder 6 collaborations

Dmitri Beglov 5 collaborations

Megan Egbert 4 collaborations

George Jones 4 collaborations

Dzmitry Padhorny 4 collaborations

Bing Yang 3 collaborations

Amanda E Wakefield 3 collaborations

György M Keserű 3 collaborations

Adrian Whitty 3 collaborations

Nasser Hashemi 3 collaborations

Mikhail Ignatov 3 collaborations

Sergei Kotelnikov 3 collaborations

Ryota Ashizawa 3 collaborations

Omeir Khan 3 collaborations

Zhuyezi Sun 3 collaborations

Sungsik Lee 2 collaborations

Sönke Seifert 2 collaborations

Larry A Curtiss 2 collaborations

Michael J Pellin 2 collaborations

Marcelo S Castilho 2 collaborations

Soenke Seifert 2 collaborations

Pirooz Vakili 2 collaborations

Ioannis Ch Paschalidis 2 collaborations

Maria Lazou 2 collaborations

Thu Nguyen 2 collaborations

Diane Joseph-Mccarthy 2 collaborations

Israel Desta 2 collaborations

Glen A Ferguson 1 collaboration

Randall E Winans 1 collaboration

Detre Teschner 1 collaboration

Robert Schlögl 1 collaboration

Vasiliki Papaefthimiou 1 collaboration

Jeffrey Greeley 1 collaboration

Nisha Mammen 1 collaboration

Leonardo Spanu 1 collaboration

Eric C Tyo 1 collaboration

Shobhana Narasimhan 1 collaboration

Christine Yueh 1 collaboration

Yang Liu 1 collaboration

Nicholas Marcella 1 collaboration

Anatoly I Frenkel 1 collaboration

Shahabeddin Sotudian 1 collaboration

Israel T Desta 1 collaboration

Shahrooz Zarbafian 1 collaboration

Matthew R Collins 1 collaboration

Boran Hao 1 collaboration

Konstantin I Popov 1 collaboration

Stan Xiaogang Li 1 collaboration

Mosavverul Hassan 1 collaboration

Evangelos A Coutsias 1 collaboration

Gennady Poda 1 collaboration

Alexander Tropsha 1 collaboration

Diane Joseph-McCarthy 1 collaboration

Ayse A Bekar-Cesaretli 1 collaboration

Zhanyong Li 1 collaboration

Ying Yang 1 collaboration

Omar K Farha 1 collaboration

Joseph T Hupp 1 collaboration

Kathryn A Porter 1 collaboration

Andrey Alekseenko 1 collaboration

Nawsad Alam 1 collaboration

Emiliano Brini 1 collaboration

Ken Dill 1 collaboration

Ora Schueler-Furman 1 collaboration

Anh T Ngo 1 collaboration

Xiangyi Luo 1 collaboration

Hsien-Hau Wang 1 collaboration

J G Wen 1 collaboration

Pedram Abbasi 1 collaboration

Mohammad Asadi 1 collaboration

Chengji Zhang 1 collaboration

Dean Miller 1 collaboration

Dongzhou Zhang 1 collaboration

Jun Lu 1 collaboration

Paul C Redfern 1 collaboration

Kah Chun Lau 1 collaboration

Rachid Amine 1 collaboration

Rajeev S Assary 1 collaboration

Yun Jung Lee 1 collaboration

Amin Salehi-Khojin 1 collaboration

Khalil Amine 1 collaboration

Jennifer Chu 1 collaboration

Wenhan Zhang 1 collaboration

Regina Cencic 1 collaboration

William G Devine 1 collaboration

Thomas Henkel 1 collaboration

Lauren E Brown 1 collaboration

John A Porco 1 collaboration

Jerry Pelletier 1 collaboration

Joseph Kioseoglou 1 collaboration

Karthika Lakshmi Kolipaka 1 collaboration

Jan Ilavsky 1 collaboration

Michael Pellin 1 collaboration

Mukhles Sowwan 1 collaboration

Panagiotis Grammatikopoulos 1 collaboration

Jonathan S Mason 1 collaboration

Thamires Q Froes 1 collaboration

Regina L Baldini 1 collaboration

Mengqi Zhong 1 collaboration

Andrew Lynch 1 collaboration

Samantha N Muellers 1 collaboration

Stefan Jehle 1 collaboration

Lingqi Luo 1 collaboration

David R Hall 1 collaboration

Reina Iwase 1 collaboration

James P Carolan 1 collaboration

Amanda Wakefield 1 collaboration

Kristina Streu 1 collaboration

Christine M Harvey 1 collaboration

Paula C Ortet 1 collaboration

Karen N Allen 1 collaboration

Usman Ghani 1 collaboration

Shifan Ma 1 collaboration

Yankang Jing 1 collaboration

Mark McGann 1 collaboration

Istvan J Enyedy 1 collaboration

Antonija Mravak 1 collaboration

Vlasta Bonačić-Koutecký 1 collaboration

Jeff Triplett 1 collaboration

Kojo Idrissa 1 collaboration

James Goebel 1 collaboration

Ernest Glukhov 1 collaboration

Dmytro Kalitin 1 collaboration

Darya Stepanenko 1 collaboration

Yimin Zhu 1 collaboration

Thu Nguen 1 collaboration

Carlos Simmerling 1 collaboration

Julie C Mitchell 1 collaboration

Ken A Dill 1 collaboration

Amanda Elizabeth Wakefield 1 collaboration

Istvan Kolossvary 1 collaboration