LM-VS™Designed Scaffold Technology
LM-VS™Designed Scaffold Technology
Translates
Molecular Motion
Into
Logical Hit Discovery
Translates Molecular Motion
Into Logical Hit Discovery
Translates
Molecular Motion
Into Logical Hit Discovery
LM-VS™ learns molecular dynamics and performs evidence-based Hit Discovery
on complex targets through AI-Designed Scaffolds.
LM-VS™ learns molecular dynamics and performs evidence-based Hit Discovery
on complex targets through AI-Designed Scaffolds.
3 Target Verification
3 Target Verification
3 Target Verification
Challenges of Hit Discovery,
The Solutions Proposed by LM-VS™
Challenges of Hit Discovery,
The Solutions Proposed by LM-VS™
LM-VS™ has demonstrated stable and consistent binding with three challenging targets:
EGFR, MDM2, and CDK6.
LM-VS™ has demonstrated stable and consistent binding with three challenging targets: EGFR, MDM2, and CDK6.
Structural Variability of Membrane Proteins
EGFR (Transmembrane Receptor)
High structural variability during activation and mutation frequently reshapes the binding pocket. Under such dynamic conditions, small molecules struggle to maintain stable interactions.
Structural Variability of Membrane Proteins
EGFR (Transmembrane Receptor)
High structural variability during activation and mutation frequently reshapes the binding pocket. Under such dynamic conditions, small molecules struggle to maintain stable interactions.
Structural Variability of Membrane Proteins
EGFR (Transmembrane Receptor)
High structural variability during activation and mutation frequently reshapes the binding pocket. Under such dynamic conditions, small molecules struggle to maintain stable interactions.
Structural Variability of Membrane Proteins
EGFR (Transmembrane Receptor)
High structural variability during activation and mutation frequently reshapes the binding pocket. Under such dynamic conditions, small molecules struggle to maintain stable interactions.
Flat and Shallow Interaction Interfaces
MDM2 (Protein–Protein Interaction)
MDM2, which interacts with p53 on a broad and flat surface, offers little pocket depth for stable binding. Such a limited interface makes it difficult for typical small molecules to achieve sufficient affinity.
Flat and Shallow Interaction Interfaces
MDM2 (Protein–Protein Interaction)
MDM2, which interacts with p53 on a broad and flat surface, offers little pocket depth for stable binding. Such a limited interface makes it difficult for typical small molecules to achieve sufficient affinity.
Flat and Shallow Interaction Interfaces
MDM2 (Protein–Protein Interaction)
MDM2, which interacts with p53 on a broad and flat surface, offers little pocket depth for stable binding. Such a limited interface makes it difficult for typical small molecules to achieve sufficient affinity.
Flat and Shallow Interaction Interfaces
MDM2 (Protein–Protein Interaction)
MDM2, which interacts with p53 on a broad and flat surface, offers little pocket depth for stable binding. Such a limited interface makes it difficult for typical small molecules to achieve sufficient affinity.
Precision Control of Dual Binding Geometry
CDK6 (TPD Warhead Anchoring)
In TPD, the warhead must anchor precisely to control orientation and distance for forming ternary complexes with E3 ligases. But CDK6's deep, narrow pocket makes stable alignment nearly impossible.
Precision Control of Dual Binding Geometry
CDK6 (TPD Warhead Anchoring)
In TPD, the warhead must anchor precisely to control orientation and distance for forming ternary complexes with E3 ligases. But CDK6's deep, narrow pocket makes stable alignment nearly impossible.
Precision Control of Dual Binding Geometry
CDK6 (TPD Warhead Anchoring)
In TPD, the warhead must anchor precisely to control orientation and distance for forming ternary complexes with E3 ligases. But CDK6's deep, narrow pocket makes stable alignment nearly impossible.
Precision Control of Dual Binding Geometry
CDK6 (TPD Warhead Anchoring)
In TPD, the warhead must anchor precisely to control orientation and distance for forming ternary complexes with E3 ligases. But CDK6's deep, narrow pocket makes stable alignment nearly impossible.
Working on a challenging target?
Working on a challenging target?
Working on a challenging target?
LM-VS™ finds the logic behind binding — and helps you apply it to your own target.
LM-VS™ finds the logic behind binding
— and helps you apply it to your own target.
LM-VS™ finds the logic behind binding — and helps you apply it to your own target.
Case 1. EGFR – Transmembrane Receptor
Case 1. EGFR – Transmembrane Receptor
LM-VS™ Solution: Stable Binding in Dynamic Structures
LM-VS™ Solution: Stable Binding in Dynamic Structures
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Why is it challenging?
Problem
EGFR undergoes significant conformational changes during activation and mutation, causing frequent reshaping of its binding pocket and charge distribution.
Conventional docking methods treat proteins as static structures, often failing to predict reliable binding modes.
How did LM-VS™ approach it?
IV (Input View)
By analyzing thousands of conformational frames, LM-VS™ identified anchor residues that remain stable across transitions and used them as the foundation for scaffold design.
Does it really work?
PAV (Post Analysis View)
Incorporating full dynamic motion into the design preserved stable interactions throughout conformational shifts. Anchored scaffolds maintained contact even in regions where binding was expected to break.
A Shift in Design Philosophy
Significance
Instead of avoiding molecular motion, LM-VS™ integrates structural flexibility as a design variable — proving that motion-aware scaffolds can achieve stable binding on dynamic targets.
Case 2. MDM2 – PPI Surface
Case 2. MDM2 – PPI Surface
LM-VS™ Solution: Shape Complementarity on Flat Surfaces
LM-VS™ Solution: Shape Complementarity on Flat Surfaces
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Why is it challenging?
Problem
MDM2 interacts with the tumor-suppressor protein p53 on a shallow and flat groove with little depth. Conventional inhibitors mimic the binding mode of p53, but lack sufficient surface complementarity to maintain stable adhesion — resulting in weak and transient binding on the flat interface.
How did LM-VS™ approach it?
IV (Input View)
Analyzed surface curvature to locate hydrophobic anchors and designed scaffolds that adhere to the contour rather than penetrating the plane.
Does it really work?
PAV (Post Analysis View)
The LM-VS™ designed scaffold covered the interface snugly, showing improved persistence and complementarity compared to traditional inhibitors.
A Shift in Design Philosophy
Significance
A protein surface is not a limitation — it is a landscape to be engineered. By aligning electronic density instead of pursuing depth, LM-VS™ achieved structural persistence even on flat interfaces.
Case 3. CDK6 – TPD Warhead Design
Case 3. CDK6 – TPD Warhead Design
LM-VS™ Solution: Precision Control in Dual Binding Geometry
LM-VS™ Solution: Precision Control in Dual Binding Geometry
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
Why is it challenging?
Problem
CDK6, a cell-cycle regulatory kinase, features a deep, narrow ATP pocket.
Conventional inhibitors strengthen hinge binding but lose geometric balance when forming ternary complexes with E3 ligases.
How did LM-VS™ approach it?
IV (Input View)
Maintained the hinge axis while re-aligning local hydrophobic networks to fix the binding direction and spatial orientation.
Does it really work?
PAV (Post Analysis View)
The designed warhead retained its orientation and balance, ensuring stable complex formation during E3 binding.
A Shift in Design Philosophy
Significance
Beyond simply improving potency, LM-VS™ proposes a structural buffering strategy — minimizing conformational distortion during degradation complex formation.
One Principle, Across All Targets
One Principle, Across All Targets
One Principle, Across All Targets
One Principle, Across All Targets
From Observation to Validation —
A Unified Logic for Molecular Design
From Observation to Validation — A Unified Logic
for Molecular Design
Designed Scaffold LM-VS™ observes protein dynamics, learns persistent binding patterns,
designs scaffolds based on these pattern, and validates their stability through AI-based simulation.
Designed Scaffold LM-VS™ observes protein dynamics, learns persistent binding patterns,
designs scaffolds based on these pattern, and validates their stability through AI-based simulation.
Observe
Tracking protein motion over time
# Target Protein # MD Simulation
Learn
Learn persistent binding patterns
# 100 Rounds # AI Training
Design
Creating structures that fit the pattern
# IV (Input View) # Designed Scaffold
Validate
Testing stability and performance
# PAV (Post Analysis View) # Binding Mode
EGFR
MDM2
CDK6
Strategy
Controlling structural flexibility
Compensate for flat surface
Balance dual-site geometry
Issues
Active–inactive transition
Flat-surface instability
Narrow pocket restriction
Observation
Track motion dynamics
Map surface electrons
Map dual-site vectors
Learning
Find stable pivots
Identify planar anchors
Learn spatial correlation
Design (IV)
Hinge-pivot control
π–π / CH–π network
Fix warhead direction
Validation (PAV)
Maintain binding stability
Enhance surface adhesion
Verify alignment & balance
EGFR
MDM2
CDK6
Strategy
Controlling structural flexibility
Compensate for flat surface
Balance dual-site geometry
Issues
Active–inactive transition
Flat-surface instability
Narrow pocket restriction
Observation
Track motion dynamics
Map surface electrons
Map dual-site vectors
Learning
Find stable pivots
Identify planar anchors
Learn spatial correlation
Design (IV)
Hinge-pivot control
π–π / CH–π network
Fix warhead direction
Validation (PAV)
Maintain binding stability
Enhance surface adhesion
Verify alignment & balance
EGFR
MDM2
CDK6
Strategy
Controlling structural flexibility
Compensate for flat surface
Balance dual-site geometry
Issues
Active–inactive transition
Flat-surface instability
Narrow pocket restriction
Observation
Track motion dynamics
Map surface electrons
Map dual-site vectors
Learning
Find stable pivots
Identify planar anchors
Learn spatial correlation
Design (IV)
Hinge-pivot control
π–π / CH–π network
Fix warhead direction
Validation (PAV)
Maintain binding stability
Enhance surface adhesion
Verify alignment & balance
EGFR
MDM2
CDK6
Strategy
Controlling structural flexibility
Compensate for flat surface
Balance dual-site geometry
Issues
Active–inactive transition
Flat-surface instability
Narrow pocket restriction
Observation
Track motion dynamics
Map surface electrons
Map dual-site vectors
Learning
Find stable pivots
Identify planar anchors
Learn spatial correlation
Design (IV)
Hinge-pivot control
π–π / CH–π network
Fix warhead direction
Validation (PAV)
Maintain binding stability
Enhance surface adhesion
Verify alignment & balance
Now it's your turn to prove at your target
Now it's your turn to prove
at your target
Experience LM-VS™, which starts with logic and is completed with data,
from IV design to PAV validation.
Experience LM-VS™, which starts with logic
and is completed with data,
from IV design to PAV validation
Features
Features
Features
Features
Efficiency maximized
by the precision of technology
Efficiency maximized
by the precision of technology
LM-VS™ sets a new standard for Hit Discovery, not just in speed, but in accuracy and validated data.
LM-VS™ sets a new standard for Hit Discovery, not just in speed, but in accuracy
and validated data.
Improved validation efficiency through minimized false positives
An AI that has learned to articulate the structure of proteins automatically excludes candidates with low binding potential, enhancing the accuracy of hit candidates.
Improved validation efficiency through minimized false positives
An AI that has learned to articulate the structure of proteins automatically excludes candidates with low binding potential, enhancing the accuracy of hit candidates.
Improved validation efficiency through minimized false positives
An AI that has learned to articulate the structure of proteins automatically excludes candidates with low binding potential, enhancing the accuracy of hit candidates.
Improved validation efficiency through minimized false positives
An AI that has learned to articulate the structure of proteins automatically excludes candidates with low binding potential, enhancing the accuracy of hit candidates.
Identification of potential binding candidates within 2 weeks
Rapidly screening a library of 10 billion compounds to identify only synthesizable hit candidates. (Enamine / ZINC / ChEMBL / SYNPLE)
Identification of potential binding candidates within 2 weeks
Rapidly screening a library of 10 billion compounds to identify only synthesizable hit candidates. (Enamine / ZINC / ChEMBL / SYNPLE)
Identification of potential binding candidates within 2 weeks
Rapidly screening a library of 10 billion compounds to identify only synthesizable hit candidates. (Enamine / ZINC / ChEMBL / SYNPLE)
Identification of potential binding candidates within 2 weeks
Rapidly screening a library of 10 billion compounds to identify only synthesizable hit candidates. (Enamine / ZINC / ChEMBL / SYNPLE)
Reduction of unnecessary experimental costs
For $20,000, we provide an IV (Input View) Report that includes AlphaFold-based structural analysis and quantitative validation.
Reduction of unnecessary experimental costs
For $20,000, we provide an IV (Input View) Report that includes AlphaFold-based structural analysis and quantitative validation.
Reduction of unnecessary experimental costs
For $20,000, we provide an IV (Input View) Report that includes AlphaFold-based structural analysis and quantitative validation.
Reduction of unnecessary experimental costs
For $20,000, we provide an IV (Input View) Report that includes AlphaFold-based structural analysis and quantitative validation.
Process
Process
Process
Process
2-Week Completion Process
2-Week Completion Process
We transparently share all stages from design to analysis
and reporting based on target protein information, completing it together.
We transparently share all stages from design to analysis and reporting based on target protein information, completing it together.
Deliverables
Deliverables
Deliverables
Deliverables
Practical Analysis Result Package
Practical Analysis Result Package
We provide the analysis results of AI-based Hit Discovery
in a form that can be immediately utilized for decision-making and subsequent research.
We provide the analysis results of AI-based Hit Discovery in a form that can be immediately utilized for decision-making and subsequent research.
IV (Input View) Report
PDF + 3D Structure File
Presents the combined structure and pattern of the designed scaffold
Analysis of protein-ligand interactions and binding sites
Minimizes unnecessary experiments by confirming and validating initial design directions
PAV (Post Analysis View) Report
PDF + Raw Data (EXCEL, CSV)
Provides quantitative metrics such as Affinity scores, RMSD/RMSF
Summary of AI screening results after 100 rounds of iterative learning
Scientific evidence materials usable for investment and regulatory responses
Final Report
Comprehensive summary of key Hit candidates and core metrics
Includes candidate prioritization ranking and research insights
Optimization suggestions for subsequent experimental design
3D Structures
ZIP Compressed File
Designed scaffold structure (SDF, MOL2)
Binding structure of protein-ligand complexes (PDB)
Includes top 10 docking poses
Pricing
Pricing
Pricing
Pricing
Collaboration Models Tailored to
Research Stages and Goals
Collaboration Models Tailored to
Research Stages and Goals
From early stages requiring rapid validation to strategic co-development,
you can choose the most efficient collaboration method based on the speed and goals of your research.
Check out the optimal program for your research stage.
From early stages requiring rapid validation to strategic co-development, you can choose the most efficient collaboration method based on the speed and goals of your research.
Check out the optimal program for your research stage.
Standard
Popular
$20,000
/ Target Protein
Recommended for cases requiring validation of new targets or HIT exploration
Comprehensive analysis package including IV + PAV + result reports
3rd-party app integrations
3rd-party app integrations
Comprehensive analysis package including IV + PAV + result reports
Rapid Hit exploration through AI-based structure design and validation
Advanced analytics
Advanced analytics
Rapid Hit exploration through AI-based structure design and validation
Advanced
Guidance After Consultation
Recommended for cases validating candidates before entering the preclinical stage
Includes synthesis and in-vitro validation, along with follow-up lead suggestions
Includes synthesis and in-vitro validation, along with follow-up lead suggestions
Includes synthesis and in-vitro validation, along with follow-up lead suggestions
Includes synthesis and in-vitro validation, along with follow-up lead suggestions
Provides optimized analysis design based on research goals and conditions
Provides optimized analysis design based on research goals and conditions
Provides optimized analysis design based on research goals and conditions
Provides optimized analysis design based on research goals and conditions
Partnership
Decision After Consultation
Recommended for cases requiring partnerships with pharmaceutical companies and institutions
Collaborative research on custom algorithms, data, and pipelines
Dedicated account & success manager
Dedicated account & success manager
Collaborative research on custom algorithms, data, and pipelines
Joint establishment of AI-based Drug Discovery systems
Custom dashboards & reports
Custom dashboards & reports
Joint establishment of AI-based Drug Discovery systems
Support Center
Support Center
Support Center
Support Center
FAQ
FAQ
Is there any information or materials that the client needs to prepare for the consultation?
Are there minimum project size or conditions?
Is it possible to request intermediate reviews or modifications?
How are costs calculated?
Is it possible to issue proof documents such as invoices upon payment?
Is it possible to get a refund or cancellation?
Can the results be used for IP registration or patent strategies?
Can it be expanded into follow-up research or joint development?
How is data security and confidentiality ensured?
Is there any information or materials that the client needs to prepare for the consultation?
Are there minimum project size or conditions?
Is it possible to request intermediate reviews or modifications?
How are costs calculated?
Is it possible to issue proof documents such as invoices upon payment?
Is it possible to get a refund or cancellation?
Can the results be used for IP registration or patent strategies?
Can it be expanded into follow-up research or joint development?
How is data security and confidentiality ensured?
Is there any information or materials that the client needs to prepare for the consultation?
Are there minimum project size or conditions?
Is it possible to request intermediate reviews or modifications?
How are costs calculated?
Is it possible to issue proof documents such as invoices upon payment?
Is it possible to get a refund or cancellation?
Can the results be used for IP registration or patent strategies?
Can it be expanded into follow-up research or joint development?
How is data security and confidentiality ensured?
Is there any information or materials that the client needs to prepare for the consultation?
Are there minimum project size or conditions?
Is it possible to request intermediate reviews or modifications?
How are costs calculated?
Is it possible to issue proof documents such as invoices upon payment?
Is it possible to get a refund or cancellation?
Can the results be used for IP registration or patent strategies?
Can it be expanded into follow-up research or joint development?
How is data security and confidentiality ensured?
Let’s Connect
Let’s Connect
Let’s Connect
Let’s Connect
Do you have any unresolved targets?
AI-based Hit Discovery that finds new possibilities in the movement of proteins. We go beyond the limits of challenging targets and let the results speak for themselves.
From Data to Discovery.
Designed with Logic, Driven by Purpose.
Contact Us
Contact Us
© Syntekabio Co., Ltd. All rights reserved.
© Syntekabio Co., Ltd. All rights reserved.
© Syntekabio Co., Ltd. All rights reserved.
From Data to Discovery.
Designed with Logic, Driven by Purpose.
Contact Us
Contact Us
© Syntekabio Co., Ltd. All rights reserved.